I don’t know anything about your setup other than what you have described, and that’s good because maybe someone can help you better.
However, having been following all of the threads daily, perhaps you are experiencing a well known issue.
The issue is that whatever you do when recording midi, before you stop the daw it is imperative that you stop Scaler first!
Stopping the daw first throws a “bunch” of data (junk) at the end of the “drag-'n-drop” midi. When you drag and drop this who knows what could happen?
So, when recording with Scaler, be sure to stop Scaler first when you are done before doing anything else. This will terminate the midi “gathering” operation.
Maybe this will help you, at least I am hoping so. And, if for some reason it doesn’t, it could still at least be a good part of the problem.
TL;DR When recording midi with Scaler always stop Scaler first, and don’t shoot the messenger. I’m just trying to help. 
Ableton Tutorial… Using Scaler 2 in Ableton Live