I have recently noticed that the likes of Zebra and Reaktor will start off in tune and then go flat by roughly a quarter tone shortly after being loaded up. Does anyone have a similar experience or any idea why this is happening.
Like a Sascha mentioned, it sounds likes it erroneous pitch bend info being sent from your controller. I have seen this happen many times on different systems using old keyboard controllers.
It's easy enough to check - you should do it if for nothing else then to rule it out.
Hook up a monitor object in your clicks and ports layer of the environment - put it in between your physical input and sequencer input. You'll see it immediately if it is happening.