Are you mixing with a sub? I used to mix bass guitar, kick and bass-drops too loud when I couldn't hear the bass that well, and I would overcompensate by turning things up too loud, which would then translate to clipping on the master buss. Also sounds like the automation you're doing may be pushing the limiter too hard towards the end like you're talking about.
Are you doing any eq or compression on the master buss? Before limiting or doing anything in your master chain, you may want to throw a spectrum analyzer (like Voxengo Span or whatever) to see if there are any frequency buildups (which sounds like there is from what you're describing). That should give you some direction as to what elements in the mix you may want to adjust eq wise, compression, limiting, etc.
Post some sample clips so we can hear what's going on and give proper advice.