When you are saying you are starting with a fresh midi track, do you mean you have opened a new project and started from scratch OR did you just start on another of the 16 slots in the TI2?
If you create a midi region and drag it from one track to the next on the TI2 and the automation is copied, it will copy the EXACT automation from the source track...meaning... if you have filter 1 automation on track 3 and you drag it to track 4, the track 4 automation will STILL be for track 3's filter automation in the virus....that will in turn confuse the virus and make the automation go haywire. I do this all the time on accident.
IF this isn't the problem and you really are working with a clean slate, my first step in troubleshooting would be to try setting the automation to latch in the drop down menu that should now say "read".... that way you can tweak the actual knob on the virus and it will write the info in for you then see what happens from there...
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