I ran into something similar before the Freeze option was available, maybe this will help..

When BIAB finds an audio file in the songs directory, program creates a .BT0 file. You can see in the Windows bar at the top left if this is occurring. It says something like "Creating beat map file" or something like that. I found that if I Save the file, even if no changes were done, the next time the song is opened and played, the beat map creation occurs again. I believe the Freeze works in a similar manner.

Rachael