I have a feeling your master boot record (MBR) has become corrupt. You could run a simple command from the repair console to rebuild the MBR and see if that fixes it.

Command is:
fixmbr

NTFS is far superior compared to FAT, there are limitations on file sizes, etc.

Another idea if you have changed the SATA settings in the BIOS from AHCI to Native, which also causes boot problems.