Midi Record Looping Acting Weird

While doing some Midi recording in loop mode, I noticed that some takes were different lengths. Some takes were of the proper length. Others were chopped at the beginning (blue). Others chopped at the end (yellow highlight). And as you can see, one was almost a whole measure short (red)! All pictures are of the same screen. The now marker is at the beginning of the top two clips, not the beginning of the measure.
 

Try X3e?

Most of that is normal. Clip boundaries start and end where the first and last events start and end. If you use input quantizing, they'll end up starting on the measure but will still end wherever you released the last note or at the end of the loop if you played a note early and were holding it when the loop restarted for the next take.  That's working as designed, but is obviously sub-optimal. I recommend looping a measure or two longer than you're actually recording to avoid this particular issue.
 
And you're obviously in Comp recording mode so end of the last clip will cause a comping split to be made in other clips at the same point. And you probably have Non-destructive MIDI Editing enabled which will leave those little slip-edited clip stubs at the end, even if they contain no data. I always have this option disabled.
 
But there's something odd going on with your take order, unless you've been dragging things around...? And I'm not sure about the clip that ended up outside the loop boundary.