I found something, at least with BIAB 2011.

I downloaded the song file and tried changing a few things. If the number of repeats is set to 4 or 5, the problem occurs. But if set to 1, 2, 3, 6, 7 the chord symbol shows up in the correct spot. Pretty strange problem.

Not exactly a fix, as the number of repeats wiould have to be set to something other than what was intended, but should be a clue to the source of the problem.