After weeks of odd pitch behaviour in Cubase I believe I have narrowed it down to my M-Audio Keystation.
I would at times get a random pitch drop which would require a reboot of Cubase to reset, my initial thought was that it was caused by the old Philip Rees CSF but I took that out the system and still the same problem. It was also occurring on the USB input which bypassed the CSF anyway.
I substituted the Keystation with my Casio CZ-101 and the problem ceased. Went back to the Keystation and the problem returned. I then noticed Cubase was showing random MIDI inputs, this was noticeable when running the Arturia Mini V as you could see the pitch bend wheel move. Dismantling the Keystation and disconnecting first the Pitch Wheel and then both Pitch and Mod Wheel did not cure the problem.
Unfortunately the small keys of the Casio and the fact it does not transmit octave change messages discount the Casio as a long time solution. Currently have the small MidiSmart controller doing the duties, once I am sure the problem has gone I will invest in another controller.