iphone6 ios 9.0.1 will not connect to itunes

I have the same problem.

One of those things. I am running iOS 9.0.1 (was on iPhone 6 Plus, now on iPhone 6S Plus) but what killed the app syncing was iTunes 12.3 on Windows 10. After that, no more syncing. It also killed iCloud in my system tray. The icon is there, you can log in with your apple id but when it goes to do the 2-step verification, you enter the 4 digits and it just sits there. I have reinstalled iTunes as System Administrator, reinstalled iCloud as System Administrator and nothing. We just have to wait for Apple to fix iTunes. Now, I have 35 apps that are waiting to update. urgh

Apple support suggested I try another computer. Went to my wife's computer. Logged her out of iCloud and tried to log me in. Same problem. Tried to log her back in, no more, same verification error. He said he never heard of that problem. Probably not but he will hear more about it from others.

Just installed iOS 9.0.2 that was released today (9/30/15). Solved all my problems with syncing apps and attaching to the iCloud from Windows 10. It is now performing the updates of 35 apps. Woohoo. fixed

Here is how I solved this problem. If you are not using Windows 10, I cannot say if this will work for you or not. This did solve my problem on Windows 10.

I am using Windows 10 and Microsoft has made things rough and cracked down on undesirable installations. You used to be able to install a program when you had administrator access and the program worked fine. Now, with Windows 10, even though it says you have adminstrator access, you are not the system administrator.

This causes a lot of programs I had not to work correctly. I had to go to the EXE file and right click on it, go to Compatibility tab and click on "Run this program as an Adminstrator" to make them work.

To make iTunes and iCloud work properly, after I installed iOS 9.0.2 (or shortly before I forget which), I went to the c:/ program files/ itunes (do not copy and paste, navigate there with your mouse). Right click on iTunes.exe, select Compatibility tab and click the run this program as an administrator. This is the program that runs when you click the desktop iTunes icon.

This is only one spot that has to be fixed. Next go back to c:/. Click on the tab at the top View (File Home Share View). Now click on Hidden Items. This will let you see the hidden files. Double Click on ProgramData, double click on Microsoft, double click on Windows, double click on Start Menu, double click on Programs

This is where the iTunes and iCloud are when your computer boots and things start loading. Do not mess with anything but the iTunes and iCloud unless you know what you want to do. Double Click on iCloud, right click on iCloud, click on Compatiblity Tab and click on Run this program as an administrator.

Go up one level to Programs and double click on iTunes. Once again, click Compatibility Tab and click Run this program as an administrator.

Now, click on c:/ and uncheck Hidden Items so the hidden files will not annoy you. Also keeps things safe as you should not mess with them unless you know what you are doing.

Reboot your computer. This should allow iTunes and iCloud read/write access to everything they need to do. After I did this, I was able to log into iCloud on the desktop (do not confuse this with icloud.com). In the system tray is an iCloud icon that allows your computer to talk with the cloud. My iPhone 6S Plus synced and I was able to update all the apps that previously just sat there in iTunes doing nothing.

You may get a message on your screen after you close iTunes from the Compatibility Checker asking if this solved your Compatibility problem. Just click yes. It will not ask again.

Just a tip in the future with Windows 10. If you want to install a program, do not just click on the setup.exe for the program, right click it and choose Run as administrator. If you do this, you solve the read/write problems caused by installing it as a User. Apple does a behind the scenes upgrade and you do not have the opportunity to choose run as administrator. Guess if there is an upgrade down the road to iTunes 12.4 etc, we will have to do these things again.

Hope this helps.