Hey guys,
While Noel was tracking down this issue, we discovered a work-around. If you're comfortable editing your registry, try this:
Go to:
HKEY_CURRENT_USER\Software\Cakewalk Music Software\SONAR Producer\Cakewalk VST [or Cakewalk VST X64]\Inventory.
Find the synth that's exhibiting this issue in that list, and select it. In the right, there will be a listing named "numInputs." Set it's value to 2. Do the same for maxUsedInputs.
Then restart SONAR and try to reproduce the problem.
Warning: Changing the wrong thing in the Windows registry can mess stuff up. So create a back up first by exporting the root, which is named "Computer."
*Edited to add info on maxNumInputs