Time Machine stuck on "Preparing backup" whenever returning from Boot Camp to OS X

Okay so I figured this out a while ago, but I'll post it here too. The problem was I was using MacDrive, which allows me to read and write to Mac partitions while in Windows (using Boot Camp).

MacDrive sometimes modified files on the Mac partitions even if I didn't open them; I think it sometimes perform optimization actions to speed up the reading of Mac partitions.

This means that when I return to Mac OS X, Time Machine notices that a Mac partition was changed while outside of OS X, so it reindexes everything to be sure it doesn't miss anything.

If you stop the backup and delete the 2012-09-30-094332.inProgress folder (substituting your exact date and time) as this will let it start cleanly as sometimes it spends more time deciding what has already been backed up partially to the Time Machine destination

If you don't have a partial backup on the destination, then you might need to look deeper at spotlight indexing issues or perhaps wait it out over night to see if the volume of files actually needs several hours to sort out.

I presume you've used Disk Utility to verify all volumes and if not, that might be a good isolating step to perform if this condition persists.