I think I've found a decent setup for cutting and encoding. I'm using mpg2cut to cut commericals, and then let mcebuddy encode the trimmed videos to h.264 overnight. I'm having some audio sync issues when I try to join 2 ts files together, but I think it's more a function of the nature of ts files than mpg2cut.
Just to wanted to let ya'll know of a setup that seems to be working for me.