Originally Posted by MarioD
It looks like you are not filtering out everything but notes. It may be beneficial to show us what is checked and unchecked in your MIDI filter. I know you said that only notes on and off were selected but somehow it might have been reset or it isn't working. If necessary I could try recording in BiaB; I normally only record in my DAW.
Another thought have you tried to record MIDI in another song? I ask because if you are only using one song over and over that song file may be corrupted.

I took a completely different song and made sure the ONLY thing checked in the MIDI filter was NOTES and it still stopped recording MIDI at a random spot in the song. Looking at the MIDI monitor it appears as if the BIAB song is generating some MIDI events. I am not sure where they are coming from. I have disabled all tracks except the ones I am using.