Theres some good news and bad news regarding this situation. first, the bad news...
The input replay code has issues, I'm afraid. To help get around these issues, here are some things to remember while recording inputs:
Start recording after the bios has booted up. bios's (neogeo, pgm, etc) do some funny things like random number generator calculation and such which will cause the input to go out of sync. also don't use savestates.
The good news:
The replay code has been enhanced quite a bit and even supports going back (re-play) w/savestates now. It will be available in the next version of fbalpha, but I'm not sure when that will be. Barry, The guy that does the releases has been MIA lately. (Barry, you still alive buddy??)
best regards,
- dink