I'm having the same problem, but I'm not sure that the backup process is actually completing. The sync continues as normal, but I get the "applemobilebackup.exe has stopped working" error just as my backup was about to end.
I'm curious, do you have AirSharing installed on your iPhone?
Reading about this error elsewhere leads me to beleive that this is an iPhone-related problem, NOT a Windoes Vista problem. Other users of Windows XP and Mac OS X are having the same problem.
Some users, like me, have mentioned having large files in the AirSharing app, so I was just wondering if that could be a problem.