Running Windows Vista 64 bit here, I've had problems a couple times and had to uninstall/reinstall. I keep getting the error "The procedure entry point sqlite3_wal_checkpoint could not be located in the dynamic library SQLite3.dll" upon trying to start iTunes. So it won't even load for me. I tried some of the suggestions found on the Apple Support Community to no avail. I have to uninstall all Apple programs and reinstall and it seems to work. Last time I think it updated Quicktime and when I tried opening iTunes last night it just gave me that same error message. So I just finished uninstalling/reinstalling for the 2nd time and seems to work OK at the moment. A quick search online seems to find quite a few people with problems. Not sure what the percentage is as there are millions using iTunes so perhaps we are in the minority.
Since updating iTunes, It will no longer backup my JB,d iPhone 4. Tried everything Apple suggested plus everything I could find here and elsewhere, still no luck. Going to try restoring and updating my phone to 4.3.5 and using a good backup I have saved. I'm on Windows 7 64 bit.
I've tried it on both Mac and Windows 7 with a JB'd 3GS and it works fine on both. I decided to keep using it on Windows 7 because it syncs with Outlook while the Mac version of iTunes only syncs with iCal.