I onlu noticed this problem when moved a project to PT from VST. When you zoom in you notice that none of the audio tracks start on the bit. Furtenlly the dely is not notichable when I record midi to audio but it is there.
I guess it's got to do with your midi setup, ie if you try to run many devices through one midi port / long cables etc... could also be conected to audio card letancy, so I've been told - but I can't see how 
My only advice is - see if it is consistent, is the dely always the same. Then follow craig's advice if not check you midi setup (fevurite midi timing in audio setup etc...)
HTH
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