I have the same problem when recording drums using Superior Drummer 3. Sometimes it works as intended if I open the plugin window and close it again, but it doesn't always help. I had to stop using the Replace recording mode to stop this, which means I have to manually delete all midi notes prior to recording from the point where I'm starting off to avoid overlaps (which gets old really fast). Seems to me like this is a bug, and I hope there's a fix for this coming soon. If it isn't a bug, I would also sure like to know what I'm doing wrong.