You know, kill the current installation and reinstall from scratch but now it's working correctly without ever doing that, which is strange. I'm not complaining but one day it's screwed up and the next day it's fine again! Weird!
Sync should restore your passwords and bookmarks but not your extensions. To get your extensions back, you need to use your backup.
So first paste the contents of your backup into the new profile folder and then enable sync.
That does work, also holding down the Ctrl key and clicking works but wanted to know if there was an extension that just did all that for the end user either out there or in the works. Would be helpful.