Do you have any of the Aux tracks in the Arrange?
1. In the MIDI thru / regions parameters area in the Inspector do you have a delay setting on the MIDI region or the Aux tracks?
2. Do you have any Tempo changes in Global Tempo?
3. Any MIDI Controllers/Synths connected?
4. Audio Interface? And what is the interface?
5. Does this happen in a new project too?