I gotta believe this is -some- operator error? Certain MIDI notes seem to… all by themselves… move around slightly.
I get the impression maybe they are shifting because of… time base? Because of tempo changes? Space aliens? The fact that the song is in 12/8 so the grid is triplets? WHAAAT? No idea.
The notes get unquantized if you modify the Tempo Track while the track’s Time Base is on Linear Mode (clock icon).
To prevent this from happening, always check if the track/tracks are on musical mode (quarter note icon on orange background) before editing the Tempo Track (see image below).
The Tempo Track and the ability to change the Time Base of tracks is a very powerful and smart feature of Cubase.
P.S.
We usually call the operator “user” 
I saw something weird like this just yesterday while making an animated gif to post here.
While moving a Note in the Key Ed it snapped to a location other than the grid. First I thought that Snap was set to Grid+SomethingElse (Cursor for example) but when I checked Snap was only set to Grid. After that Snap worked normally. I just shrugged it off until I saw this post.
I dunno… I think there’s something else. It’s as if Cubase is getting confused between triplet grid and 4 grid.
You said that the notes “move around slightly”, but didn’t mention when.
Do you by any chance use this window in the Score Editor?
If so, you shouldn’t hit “build”, but “quantize”. This will keep the notes where they are in time and change only the display quantization.
Also, if you really need a solution to the problem you’re having, you need to be more specific. If I can’t reproduce the issue, I can’t find a fix for it. It might be just a bug, or not…
I think I’m really good with tempo/quantization related issues, but I can’t help you if I don’t know exactly what you’re trying to do.
Thank you. But that’s not it. I’m using the Key Editor. Sorry for not being more specific.