And........ Ive just down loaded Lightroom (Adobe, $124) and LRtimelapse (free). Its all freaking awesome for time lapse, have a look at the tutorials
http://lrtimelapse.com/. It has tools for correcting the exposure jumps with manual cam changes and all kinds of other TL tools and it looks to be very comprehensive and easy to use. Going by the TL forums, its now by far the best way to produce jump/flicker free TL.