Persistent issues after doing a CLEAN install of Sequoia

I don't have specific solutions for those two problems because I don't experience either of those myself. That said, you indicated a "fresh install" of the MacOS. It is very likely that the MacOS itself was fine on your Mac -- it is in a sealed, read only volume (a snapshot, actually) and cannot be altered by you and anyone else. What is much more likely is that something installed is causing the conflicts that you see.

A true "fresh install" is much more drastic than the steps you took, which simply reinstalls the MacOS but leaves everything else as it is, including whatever that is installed that is conflicting. A true "fresh install" would entail erasing/formatting the drive, installing the MacOS from Recovery, and then on first boot up, migrating only user files from a backup, but nothing else, so what is installed consists only of Apple programs, no third party software or extensions. Then I would check that Mail and the watch work as intended. If not, there is a hardware issue.

If they do work, then the next steps are to reinstall third party software and extensions one or two at a time and retest until you find the culprit that is causing the conflict.

One way to avoid all this is to download and run Etrecheck, a free diagnostic utility. Post its report here using the Additional text button below. How to use the Add Text Feature When Post… - Apple Community

People will look through the report (which provides no identifying info) and help you remove the culprit.

jedimasterkyle88 wrote:

Now I'm wondering if resetting and wiping my Mac to factory would be easier than hunting for all of the files and apps that might be interfering with my issues...

I backup my Mac to TM every day. If I wipe my Mac and restore from TM, I'm not gaining any ground since the apps or files that are causing my issues might be in the TM backup right?

That is a rather brute force approach but it works when other efforts have failed. Following the Apple instructions for how to prepare your Mac for resale basically restores your Mac to the state it would be in when brand new, with only Apple apps installed as part of the MacOS, and no user accounts. On first boot up, it will ask if you wish to migrate from a Time Machine backup. If you say yes but choose to migrate only user accounts and files, and NOTHING ELSE (do not migrate over settings, for instance, or any other misc items), it will simply recreate your user account, bring over all your user files (Documents, Pictures, Music etc.), but no other settings nor software. I would then first check how Mail behaves and verify that the issue is gone. Then installing apps and software 1 or 2 at a time and retesting after each install would be a way to proceed.

Before doing anything major like this, I would recheck the point that Zurarczurx brought up. If your email is IMAP, GMAIL, Microsoft Exchange, or the kind where all devices receive emails at the same time and are synchronized, it is possible that another of your devices using that same email account is receiving the email first, maybe by just a fraction of a second. The device could be in a different location or on a different network. When that happens, because the email has already been marked as "read" and "downloaded," Apple Mail might not make a new mail sound because it recognizes that the mail has already been received and downloaded, hence not "new."

The way to check Zurarczurx's suggestion is to shut down or close email on all devices on that email account except your Mac, and see if the sound returns. I recall noticing this when getting GMAIL and MS-Exchange email on two Macs, only one of the Macs would make the new email sound when the email had been received on the other one first.

So there are some installed items that COULD be causing you trouble:

(1) Freedom utility -- I am not familiar with this software except that I know it is intended to "eliminate distractions" ... could it be configured to eliminate some sound distractions such as email notifications. I don't know but I am suspicious of it, as it seems to duplicate the built in (and safe) Apple "Do Not Disturb" settings. Such duplicative functions can lead to conflicts and then some things just stop working. Maybe it is keeping your Mac from responding to the watch or preventing "distracting" notifications that you really do want.

(2) I see some signs of VPN being installed, which I think is a bad idea. Not sure that is causing your issues but VPNs conflict with all kinds of things and serve no purpose unless you are using an employer VPN to access a closed network.

(3) CCLEANER -- these "cleaning" apps can remove key files that are needed for the MacOS to function properly. They can't modify the MacOS itself as the MacOS is in a sealed readonly volume but if certain configuration or settings files are deleted or "cleaned," all kinds of malfunctions can result. I would uninstall this immediately, completely, using a vendor provided uninstaller.

(4) CleanMyMac -- see comment above for (3). Very bad idea to have such software, and you seem to have two of them. A complete uninstallation is needed. Unfortunately, some have reported that uninstalling does not remove all the pieces, which remain and continue to do harm. There are MANY reports in Apple Discussions about problems caused by these "cleaning" apps and difficulty in removing them. The worst situation is that something like CleanMyMac is installed under an earlier MacOS and then under a later MacOS all its files cannot be removed because the later MacOS has restricted user access to certain directories where access used to be allowed. Hence making it very difficult to completely remove. These programs, like anti-virus software (which also is not needed) are insidious in this way.

You could try booting into Safe Mode to see if your problems go away. If they do, that virtually proves that something installed is causing the problem. But something removed by the "cleaners" could still be causing misfires, even in Safe Mode. Another thing to try is to create a new user and see if the problems persist. If something user-specific is installed that causes the problem, a different user MIGHT not experience it, but it's not a 100% certainty as it could be a system-wide problem caused by something installed.

jedimasterkyle88 wrote:

I use an app called "Freedom1. " to block certain websites from being a distraction. Whether it's news, social media, or time wasters, I use it on a daily basis. I have it setup on my Mac to block very specific websites that have zero interaction with any Apple domains. I suppose I could contact their support to see if maybe their app could cause issues with Mail.

2. I use a VPN daily on my Mac and that wont change.

3. What "Vendor provided uninstaller" would you recommend I use to remove CCleaner and CleanMyMac? I'm not opposed to uninstalling those apps but I would like to uninstall them correctly instead of not.

I read through the Etrecheck report and tried to identify things installed that somehow MIGHT be conflicting with this built in function of the MacOS for Apple Mail (sounds to notify that new email has arrived). I have no insight into how these conflicts instantiate themselves, but something to block "distractions" sounded like a candidate.

Maybe others with more experience than me will see something that I missed.

You can certainly keep using VPN but then will have to cope with any issues that stem from their use. They do not provide additional security. They are akin to hiring a guard to watch your post office mail box who goes through and reads all your mail while he/she is guarding your mail box. Note that Apple says to use an Apple Watch to unlock a Mac requires that they both be logged in to the same Apple ID, and are on WiFi with Bluetooth on. VPNs can interfere with or impact networking and over the air communications with a Mac.

You would need to see if the companies that provide CCleaner and CleanMyMac also provide COMPLETE uninstallers. Just moving the app to the trash does not uninstall all the background pieces that can be running upon startup or in the background.

Your Mac is showing behavior that NO brand new out of the box Mac exhibits. Sequoia is in widespread use and as far as I can tell, where I work where hundreds of Mac users are using it, Mail sounds still are clearly heard. It is very likely something that is installed, but you seem to be defending some of the possible suspects. If you prefer, keep using them and live with the no Mail sound. I also suggested some diagnostic steps you could try, not sure if you tried them (Safe Mode, new user, etc.). Frankly, having such a software conflict is way preferable to a hardware problem because you can resolve software conflicts by removing the culprit. I would suggest as best you can, completely uninstalling all these items as a diagnostic step to see if the problem goes away. If it does, you will know one of them is the source of the problem. You can always reinstall them. This is a troubleshooting step.

But the "cleaner" software may have residual effects long after uninstalling, hopefully not in your case.

Ah - ok. 

In my experience if you've got multiple Apple devices in the room (i.e. on the same network) all yours, which all get the same email, messages and other stuff then whether or not the Mac notifies is pretty random for me. I just tested the Mail sound when I read your post (I normally have it turned off) and it didn't work for the first couple of mails I got but it worked for subsequent ones.  Notifications on my Mac often won't work if I send a mail to myself to test things, even if I send from a web interface instead of on of my Apple things. Have you tried turning off all your devices (or putting them in airplane mode) and just seeing if the Mac then notifies? It won't necessarily fix your problem but it might help you understand it.

Re-mail sounds: I don't understand the issue. If you turn on sounds in Mail settings then you get a sound when you get a new Mail. Is this not what you want? What would you gain by having a sound option in Notifications too?

See my earlier post. I enable Mail sounds for new mail when I read the OP and since then I've had 9 mails and only two of them have made a sound. Messages is the same - some do, some don't. There's no logic to it other than what I've written in my earlier post.