Solved. I changed two things. First, I noticed when I accidentally deleted a note that there was a second underneath. This turned out to be the case for all the notes so something is up with my keyboard possibly (becuase I notice the same issue when I record directly to Logic Pro on the Mac). So I cleared all the duplicate notes.
The other thing I did was relaunch Logic Pro.
Everything seems to be fine now. I don't know if either of those two changes had anything to do with it. Not sure I have any time left to use it this week now that I've solved the issue but I'm looking forward to playing with it a bit more.