Whats up Rach, hope you're still reading this haha.
I just started using loops on the MPC myself. (I'd chopped em up but not really used them in song composition) Check out my first track using a loop at
http://metro-bands.com/audio/synful.mp3
My guess about your "loop mode only" trouble with the sample is that it could be fixed by adjusting the To: field on the loop page (the left number, not the right one) a few clicks in, or padding the beginning with extra blank sound. I've fixed a few loop issues this way. Not quite sure why it happens. The envelope, filter, resonance, and tuning should maintain their settings across every instance of the note. The Program settings are applied AFTER the Trim settings, so they can be used as a default override of sorts. These settings will be applied to looped or unlooped sounds. Period.
Another thing to note is, try using Note Off for the voice overlap setting and turn off the Loop parameter in the Trim settings. This allows you to do more interesting stuff with the loop, like cut it off early or stutter it into a segment. Just like Loop mode, hold it down as long as you want it to play, only it won't automatically play again while the pad is down. For triggering full copies of the loop sound, use the regular note-triggering Mono for self-cancelling samples and Poly for crazy echoey doubling of the loop, which could be useful if programmed correctly.
I'm now pretty well versed in the ways of loop-fixing on the MPC, so hit me with any problems you do encounter here on out.
-thynctank