Actually, there's a Cubase bug that a lot of us are waiting for a fix on. That may have something to do with this, especially if you're using something like
the Midex 3 or 8 "time-correcting" MIDI interfaces:
http://linux1723.dn.net/forum/Forum16/HTML/000541.html
It causes MIDI tracks to be shifted in time after recording and before playback, and it _is_ a pain in the ass.
I was recording an E-drum track yesterday, monitoring the Cubase click and the reference audio tracks in real time. I finished the track, and went back to give it a listen- and Cubase had decided to time-shift the MIDI forward by about 2.5 measures!
It was an easy workaround, because I could just grab the track and slide it to line up properly- but that's a pain to have to do. It also appears that the offset varies- it is often 0, in fact. But you have to check each track carefully. It's not clear what causes the tracks to slip, although power-cycling the Midex seems to help fix it for a time...
For the time being, I'm always recording some lineup clicks in each MIDI and audio track, until they get a solid fix for this. It appears to have cropped up in 5.1...