goneburger

Changing to the new theme didn't help the issue either.

It's not a graphic card/video driver issue, it's all internal to Sonar. I've installed every nVidia driver for pretty much ever (years) and this bug has reproduced on all of them at one time or another since the first release of Platinum.
 
I haven't seen it in the last few weeks, but I see no reason to believe it won't still happen.  I suspect it has something to do with how Sonar remembers/tracks the zoom level for a MIDI clip and the track it's in.  Since dragged into MIDI clips don't have that out-of-band data it showed up there first, they made some changes in that area and claimed it was fixed, but I think it's still possible for a MIDI clip/track to get in that strange state.  Perhaps because of editing operations, maybe even editing outside of the Piano Roll?  If it was easily reproducible perhaps it would get fixed, but the exact steps to make it happen aren't obvious.

Sorry. I'm still on X3 where there's no issue. I'll just leave quietly.....

Tripecac
This bug is still present in 2016.05. 
 
Has anyone else noticed it?
 
Has anyone else reported it?

It's happened to me a couple of times recently. I haven't reported it as I can fiddle around and it'll sort itself out. The first time it happened I was a bit freaked out as I thought I had transposed the midi and had no idea how I'd done it.

It does strike me that it is completely unnecessary for it to go wrong.

Grum.

it happens. 

I've experienced this issue in Sonar for years. Definitely a Sonar bug.

I saw it just the other day. Seems to be related to zoom level in some way.

This might be a stupid idea, but just to be on the safe side:
Have you checked that "Snap to Scale" is deactivated?
=> https://www.cakewalk.com/Documentation?product=SONAR%20X3&language=3&help=EditingMIDI.40.html
 
"Snap to Scale" aligns grey rows with those keys that are not within the set scale. As a result, grey rows and black keys have nothing to do with each other and can be "misaligned" completely ;-)
 
If I set "Snap to Scale" to F# major, wouldn't the piano roll look exactly the same as the screenshot from tripecac from post 1?

It's not a snap to scale problem.  It fixes itself if you zoom in or out using the vertical zoom buttons.  Snap to scale would continue to stay no matter what the zoom is.  The two parts of the window (the keys on the left and the rows on the right) are just not in sync when this happens.