Hello Azslow3!
Thanks for all your help but I think I cracked this one now. So I was thinking that this little bugger acted more like a feature than a bug, so I launched the standalone version to ensure Sonar wasn’t doing something under the hood. Well I got the same behavior in the standalone version but it also added a error message to the equation.  The message complained about not finding any disk in my J: drive (which is one of my USB ports), so I thought…  “What could Zeta possibly be searching for?”. Well the obvious answer was PRESETS. So I right clicked one of the preset selectors and there it was, my version of Zeta had Next/Previous Preset mapped to CC1 (Modwheel). I removed the mapping and everything works just fine now.
 
But that leaves us with another question. Why is zeta looking for presets on my USB ports? Isn’t it supposed to look in /Cakewalk Content/Z3TA+ 2/Programs. Another question is… Is it possible to restrict Zeta to only look for presets in a certain place. I looked everywhere but couldn’t find any .ini file and there’s no options in the GUI either.