[daeron80]

Well, it sounds like it's not working right, one way or the other. Until you figure that out, you could try deleting the unwanted data before recording the new. If that doesn't work, disable automation on that track, make a new MIDI track with the same output designated, record the automation there, then copy and merge-paste it into the original track. Not saying that's a permanent solution, but it might keep you moving until it gets straightened out.