And found!
One registry key only, the W32Time service registry key. BUT the keys themselves are fine. This is a bug in Windows that I just found. If the permissions are changed in anyway on that registry key then the UAC will not give the taskbar the permissions it needs. If the UAC is off it isnt a problem.
If I change the permissions back manually it will then work again.
So you can replicate this on any windows 7 machine. I have attached a screen shot of the default permissions.
Go ahead and change one of the permissions, give users full access, or add everyone to the permissions and you will see the UAC will nopt give the taskbar permissions, now, without even rebooting, put the permissions back to what they are like in the picture (By the way each time make sure you put a check on replace all child objects and hit apply) and once put back you will see the taskbar can sync again, without even a reboot.
So this seems to be an odd bug with the UAC, makes me wonder what else it has a bug like that with. So the fix will be for me to change the permissions repair to put the defaults on that key. I will do that in the next update
So remember, even if you have this happen you do not need to reinstall or do a system restore. Time sync still works when it runs on its own, it is only the taskbar clock that wont do it as long as the UAC is on, and we know how to fix that.
Shane