Multi Monitor and Sierra Forgets Window Positions after Wake Up From Sleep

Yes, I agree, definitely a bug. Just woke up my Sierra system a few minutes ago and same thing happened, everything got pushed over to my primary monitor and I have to take the few minutes and drag stuff back over to the 2nd monitor. I also don't want to use Displays have Separate Spaces option as that effects other things in my system that I don't want.

It doesn't happen all the time, and absolutely never happened in El Cap or Yosemite or Mavericks. In those operating systems I also never had Displays Use Separate Spaces turned on, yet it still worked.

I suspect this is another one of a long list of bugs that Apple will never fix. I'm still waiting for a proper mouse wheel acceleration fix that has been happening since Yosemite.

I have just learned to live with it. Sierra has several buggy things like this which the average user doesn't notice, and I think Sierra so far has been a step down from Yosemite and El Cap. At work I made a big push to get everyone upgraded to El Cap but I won't be making that push for Sierra. Just too many goofy behavior things like this multi monitor issue that sadly I don't think will ever be fixed. I have been to the Genius bar with all of these below problems and have gotten basically a shrug from the guys there - nothing against them, but since they had no idea how to fix these issues even after I replicated it for them, it's obviously something inherit in the OS that nobody knows how to fix.

Here's a short list of some other issues I have:

• Sierra is confused about active directory passwords and desperately wants your AD password to be the same as your iCloud password. I am asked every morning to "continue to change my iCloud password" so it matches my AD password, something I will never do.
• Funny enough, any changes to my iCloud preferences pane requires the usual "type your password to continue" - and absolutely none of my passwords work in that box.
• Mouse scroll wheel acceleration is a disaster with no way to find a happy medium between the scroll speed on your trackpad vs the scroll speed on your mouse wheel. Even with a Mighty Mouse it's not the same.
• Siri on the Mac in a work environment is massively impractical unless everyone closes their door and has their own office. All of our Sierra users in the office have tried Siri and absolutely none of them use her in their day to day.
• Window focus switching is goofy. I'll be in Photoshop, open a Finder window to drag a new picture into Photoshop, just to find that Photoshop suddenly jumps to the front as soon as I start dragging the files, obscuring my new Finder window. This happens regularly in several apps both Apple and 3rd party.

As far as the Genius bar's handling of my issues, their standard approach is to "Create a new user and let's see if that continues to happen" but that is not practical in an enterprise bound Active Directory environment, because your computer account is tied into your AD account. As soon as you start talking anything enterprise with them, they won't be able to help you much, it's just not their forte and sadly there isn't any other support option. Our Business Store and Joint Venture contacts are helpful and sympathetic, but in the end they're sales guys, not hardcore apple enterprise technical support engineers.

I've always thought that solution was a bit of a cop out because they're basically saying "I don't know what it is so lets start with a fresh set of preference files and see if the problem occurs again" instead of "We've identified the problem and it's with these system files, so let's fix those instead of starting over 100% fresh."