I don't know the answer but I have a suggestion. First, a loop is designed to be hung drawn and quartered and still retain it's duplication properties. So there's a step missing, you haven't told it to become a static clip and to stop being so clever. I suggest doing all your trimming and then Bouncing it. The Bounced version should now be a normal, 'dumb' audio clip and you should be able to dupe it without any misbehavior.
I'm had the same trouble with a MIDI measure, I trimmed it back to half a measure but I can still hear the other half ringing into the next chord because trimming the clip doesn't trim the contents!
I had to Undo, shorten all the notes to half their duration and then reduce the clip size.