I've battled with this a lot in the past. I've decided that it's due to large .FLAs with LOTS of audio files.. Prowlies was really difficult to work on at the end, with 25-60sec lag not only between undos, but also selecting frames, library elements, etc. Because of this, I'm now in the habit of breaking up my .FLA into smaller, more manageable chunks (like Crumb said). Now that I'm using Flash CS3 though, I haven't seen it for a long time, even on Waterlollies (I also think my Boxxtech workstation helps) which admittedly I had split into three separate chunks.
In this current D&D job I'm on, there's a ton of separate audio clips on the timeline and loads of library symbols. At the worst of times I get an undo lag of 1-3 sec. I'm not 100% certain that lots of separate audio files are to blame, but if that sounds like a likely culprit, maybe you could try exporting all your audio as one single file, then importing that to the timeline (instead of having lots of little ones).
ya i put all the audio together into one file sometimes which helps but then that makes the file an easier target for after sound
