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