I am not exactly sure what is going on here but Studio One (4.1.1) is deleting my MIDI notes as I am recording and I think it may be related to my ATOM. This is becoming really frustrating. I've been using Studio One for a while and never had this problem until a few days ago. I've unplugged all of my gear, tried everything one at time, and restarted my computer several times. I did not have this issue until 4.1.1. Any time that I have gotten it to stop, the problem returns when I attempt to use my ATOM pad to record and lay down some notes. I've reinstalled the firmware on my ATOM as well.
Here is some footage of what's happening.
Also, if I unplug any of my MIDI devices while this happening and Studio One is open, it freezes and I have to force close it.. Please look into this PreSonus.