I have a recurrent and unpredictable problem when loop recording audio.  Most of the time it doesn't happen.  After pressing stop on my control surface, after maybe 4-5 takes, I get something like this:
 
https://twitter.com/worralljc/status/560250937802235904/photo/1
 
Instead of each take starting at the beginning of the loop point, it starts in the middle and then the end of the audio is at the beginning!
 
The only way to avoid trashing the takes is to line the audio up by hand.  
 
Has anyone else seen this?  I reported it to Cakewalk last March but they did not seem to have seen it before.  Unfortunately it took 4 months to get an email reply so I kind of gave up on them.
 
Windows 7, X3e, Konnekt 24D audio interface
 
Thoughts?

Yeah, I had the same problem. I was able to compensate for the botched start times of the looped recording by setting the punch-in/out time to the section I wanted to record and starting the loop area two measure before and ending it two measures after the punch-in section.

OK.  So basically leaving a two bar buffer of unrecorded audio around the actual part you want to loop record. 
 
I'll try that.
 

I don't know if it applies here but there have been some posts about this or something very similar and it was being caused by the count in coming into play on loop record. I think the solution was to disable the count in by setting it to 0.