Kristen,

I was having similar problems over the weekend, albeit in PT rather than RB.
After tapping in the bars, I noticed I missed a measure early on and tried to tap it in retroactively, which didn't work. The bars started jumping around and who knows what else. I started over again tapping from beginning to end and had PT change the time signature at the beginning. So PT asked me but not you. Maybe it has something to do with the lead-in. Beats me. But that worked. As Bob suggested, it helped to slow down the tempo.

Good luck.
Percy