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.
 

According to your footer you are running X3D, please install X3E which resolves some looping bugs and give us some feedback I suggest. Cheers :).

Try X3e?

OK footer updated. And yes this is happening in 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.

Just another quick question (sorry for asking the obvious). Was this a brand new X3E project, or did it this project start in an earlier version of X3 and then got opened into X3E later? (Of course you created the loop itself in X3E). Thanks...

Thanks for that response b-fly. No, I didn't move anything around. The take numbers are strange, good you noticed. I did start the take and for some reason I stopped it and started it over. Other than that, it was all one take.
 
@Alex: Yes new project. Only BFD Eco, EZD, and GR5.
 
This is what I was doing:
 
Needing a hi hat trk that varied from section to section, I thought I could record in loop mode and let it repeat four of five times and from those takes I could clip and past things together that would give the varied results I'm looking for. Once I stopped recording and looked at it is when I realized something wasn't right.
 
I have since worked on a cloned trk and straightened out the clips to make them the length I need.