Thanks for these answers, it is very helpful.

For the forced accidental issue, it was an A sharp and the song is in the key of G. That key doesn't have an A sharp or B flat, so no reason the key should have forced it to be flat. But, going back in the song now, the "forced accidental" option is allowing me to change it to A sharp. Not sure what changed.

The repeats issue was not at the end of the song. It was at the end of the first section (the A section repeats, then the B section repeats). It put the gray measures after the repeat symbol and then I'm not sure what was going on. I haven't figured out how to turn off the real tracks so I just heard like 2 versions of the real track over each other, apparently repeating from the beginning and playing the gray measures at the same time. Anyway, I solved this by just abandoning repeats and I just duplicate the whole section and key in the chords and melody twice. It's a pain but it gives me the backing track so in the end I have what I need.