Hiya,
This could be a few things,
1 if the not lining up is constant, ie; every recorded note is late by the same amount, then just select the whole Audio track, Hit ‘j’ to turn off the snap to grid and line up the 1st note. You may need to move the audio event’s snap point if your going to be quantising or moving it around the grid any further.
To avoid it next time check that the record delay offset option in the device setup window is ticked. If it is there’s also a way to specify the offset you want in samples if your interface isn’t reporting the correct latency to cubase.
Easy way to mesure the exact delay, change your timebase in the transport panel from bars and beats to samples, then use the range tool to measure the distance from the MIDI to Audio, if you have the info panel open at the top of the arrange window it’ll tell you the selection length in samples and you can type that figure in and problem solved.
2 If the offset isn’t constant then you may have a MIDI timing issue and they can be harder to track down. Make sure you are using the correct MIDI port (there will be several in the list) I can’t remember which to choose but best bet would be to work your way through the ones you aren’t using now. Once you find the one that works you can hide the others in device panel. If that still doesn’t sort you I’m all out of ideas, the last time I had to deal with issue was way back in SX days when steinberg ended up adding a MIDI port enabler file that you had to move from the application folder to make the ports work… try searching the MOTU website…
Good Luck,
PC