As far as I remember, Pro Tools is sending on the beginning of a song the program message to all the midi tracks on bar 1 (beat1). If you set the program change "none" on the midi sequenced bassdrum track, there will be no delay anymore, because your midi device hasn't to handle with the extra program change on beat 1 and the bassdrum also on beat1.
Maybe you could try and move to sequenced bassdrum hit on bar two (only for testing) and see if the timing is better on the second bar, when you start recording on bar1).
If this is the case, then it would have something to do with to many midi informations (prg changes...) on bar1/beat 1. Just start recording in the beginning and see where the bassdrum will appear in bar2.
Hopefully this helps,