I used TrueCrypt to encrypt the entire system disk for a Vista x64 installation. Everything was running fine on this, until suddenly I started having frequent (every 40-50 minutes) crashes. I had just installed Visual Studio 2008, so I thought perhaps the SQL Express instance it installed was causing some incompatibility... but after disabling those services, and in fact removing every piece of VS 2008, I was still suffering the crashes.
Finally I waded through the recent updates and noticed that Windows Desktop Search 4.0 had been recently applied. I can't prove this, but I think I may have rebooted (and hence the service got started) during my application updates. Regardless, I stopped and disabled the service and have had no crashes since.
I did set Vista to record crash dumps, but it always fails to load the crash dump driver, and so I was not able to capture any data about the crashes I experienced. Has anyone else experienced problems with this combination of applications? The system drive has a single partition and is NTFS-formatted within the TrueCrypt container, for what it's worth.