Sonar Interface controls mapped to CC#6 work fine, and the VSTs when run in standalone mode work fine with that CC#. I seem to remember reading (long ago) that certain CC#s need to have some setting (RPN? NRPN?) diddled with in order for them to work properly in Sonar. I've mapped these VSTs (S-Gear, Amplitube, Guitar Rig) up to CC#36 (Korg nanoKontrol) without other problems.
 
Very strange. Anybody have any ideas?

I can confirm that I see the same (tested with Sample Tank).
 
CC#6 is "MSB Data" for (N)RPN. I do not think that should be a problem till VST support (N)RPNs assignments (in that case such response is logical).
 
But I can suggest to avoid "well defined" CC numbers, especially if they can be used in (N)RPNs (CC#6 , 96-101). See http://www.midi.org/techspecs/midimessages.php

I seem to remember that there was a workaround. I've submitted this to support so maybe they'll know.

Also, this is not a problem in LIVE, so it has to be a SONAR thing.