Weird midi transpose issue...

I have had that sort of thing happen with Native Instrument's Reaktor.
 
I think it turned out for me to be because the particular ensemble freaked out due to a Sonar setting that zeroed out all controllers on stop.  It made the pitch drop a whole step.
 
Could something like that be occurring?
 
Once I removed that check box in Preferences>Project>MIDI, I stopped having that problem.  Please note that this is set at the project level, so IF this change is something you want to change for all future projects, you would have to make the change in your Normal project template (or whatever templates you wanted to apply the change to).
 
I hope that's what is causing your troubles, and hope the above takes care of it.
 
There are also sometimes things tied to the mod wheel, like volume, and other things you wouldn't think would be set up that way, so maybe something along those lines is occurring.
 
Lastly, there are also Key Switches for some synths, and these can be quite different for different presets for a particular instrument, such as different string patches in Kontakt.  Many of those have certain alterations of the sound tied to the hitting of particular keys.  I found that out the hard way too.
 
Bob Bone
 

Thanks guys.
I'm using DimensionPro, and it only seems to be happening on a single instance of the instrument.  Changing the global midi settings didn't stop it.  I was playing around with the octave +/- buttons on my controller keyboard during my session, maybe I hit transpose by mistake. 
I was just thinking it would have to show itself somewhere, like the event list or changes on the synth UI.  Great suggestions...I'll keep at it.
V

It does seem a bit odd that it would stay in the altered downward-transposed manner though, from a pitch-bend controller event, which is why I was thinking it could be a zero-controllers consequence.
 
To the original poster, please post back with what exact Dim Pro preset you are using on the track exhibiting this wacky altered pitch behavior.
 
Thanks, 
 
Bob Bone
 

Well, you can try to remove the check box from Preferences>Project>midi>Zero Controllers When Play Stops, and see if that helps.
 
Bob Bone