I had this issue after running the Bitlocker Drive Preperation tool.
After this i ended up with two partitions:

C: Partition of 1,5 GB (for boot files)
D: Partition of 148 GB (Windows and everything)

My BCD (former boot.ini) showed the right stuff but somehow my Windows still wouldn’t boot.
After starting up with a Windows Vista install CD and choosing “Repair my computer” I could access a command prompt.

After executing bootrec /fixboot my machine booted properly and my machines is bitlocker ready 😉