ibartley
Well I thought removing TTSSEQ.ini and restarting solved the problem but that's not the end of it. I'm losing the ability to input midi data everytime I stop and restart Sonar. 
So here's the senario:
1. Load VST into Track 1 (Simple Instrument Track)
...
You stated earlier that you traced the problem to NI Reaktor Monark. Is that the VST indicated in step 1, or is it now any VSTi?