It does happen when just bypassing a plugin, also. Basically, as the track s playing, I am A/B'ing different plugins or plugin settings. This should be a basic, standard procedure as far as I know.
In Sonar 8 Producer this process was seamless (Occasionally a minor thump but, nothing major). Starting with X3 and now with Platinum, it's terrible. I guess I'll have to stop/restart playback any time I want to try out any plugin changes while mixing. That goes completely against the whole concept of being able to A/B the effects of different processors/ settings, though.
Now, sometimes it works fine. You just never know which plugins are going to do it and which aren't.
Also, most of my projects are 16 to 20 tracks and,I don't ever use a ton of plugins.