Definitely sucks...I've been there, but it seems to work like a charm, especially when you notice little weird bugs that no one else has. Look into Sashimi for backing up your device settings for future flashes too.

My suspicion is that whenever we flash a ROM with a major build change - WM6.1 to 6.5 or Manila 2.0 to 2.1, etc. that we're running a higher risk for bugs and whatnot that might call for a "stock flash" procedure. ...but that's a stretch guess. Some folks are definitely lucky and never have issues, but it's a trend I've noticed.

PM me if it doesn't work out. ...don't forget all of the hard resets in between and after.