Hi John255,
Not sure if this will help but I found if your song has been created solely within BIAB the lead-ins are saved. On the other hand if you were to say import a MIDI file and save it the lead ins would not be saved. Also you could check settings under - "OPT/Preferences/Count-in/Met" and see if that will work for you.

If you import MIDI files you can select a BIAB style for the song and that would also solve the problem. When selecting a "style" you will get a dialogue box pop up stating that the style has been disallowed. Do you want to allow it" just click on YES.

Good luck - Hope this has helped

Carpe Diem