I've run in to this too Bob.
One thing you can try to do is raise your Midi Playback buffers.
Go in to Preferences, Midi, Playback And Recording, and raise your buffers there. Apply, exit Sonar, and restart it.
The other thing you may have to do is a live bounce. I had a couple projects that no matter what I did every other beat of the Hi-Hat would be skipped.
Another tip for freezing Session Drummer 3 is, go in to the Mixer in SD3. See the icons of the drums/cymbals/touchpad ... right click on the ones you are not using and select 'Unload'. Those will be skipped when you freeze or bounce. Otherwise, all 12 tracks will go through the process of being frozen, even if they aren't being used.
Good luck!
Bub
(Former fellow New Jersian) :)