Unfortunately it's a hardware problem with the HTC devices, most seen in the Thunderbolt and Droid Incredible 2. (I have the Incredible 2.) Even with this issue there are a few things you can do to help the performance. First limit how many layers are turned on. It's the redrawing of the gis data that causes the choppiness. The other much more useful feature is to limit how far from the rda the gis data is drawn. To do this hit Program Options - General Preferences - Performance Tweaks - Gis prozimity filter. The lower the number of degrees you choose the closer to the rda the gis data will be clipped. I run 1.5 on my Incredible 2 and get good results. Also, if they are not already checked, try hiding the counties/states while panning/zooming. This also helps.
These should help out quite a bit. But if it still doesn't satisfy you I'm sure you can contact Joe and see how he can help you out. Here's a
link from the pykl3 forum to email Joe.