I've found that one particular note keeps randomly being deleted when I cmd-tab away from the app. It seems to happen after a bit of time has passed, but I'm not sure how much time or whether it's consistent.
I tried to copy it to a new note, but not it just deletes both!
Are you syncing with Dropbox, Simplenote, both or neither?
How many machines do you run nvALT on and are they syncing simultaneously when this happens?
No. I only run nvALT on my main Mac. I do use the Simplenote on my iPhone and iPad.