My issue may be related. I'm using BIAB Mac 2012.5 Build 65 and find that if I set a tempo change using bar settings for a specific chorus it has no effect on tempo. The only way I can effect a tempo change using bar settings is if I apply to all choruses. But at least this seems fairly consistent.

And, like you I did notice that the tempo for the entire song sometimes changes when I change the tempo in the bar settings so that if I replay the song I have to reset the song tempo. Essentially the tempo doesn't reset to the song tempo when playing the song stops. I would prefer that the tempo resets to the song tempo when play stops.