I believe it's simply settings (I tested this at different tempos on a full song).

Go back in the thread to the picture I posted of the loop selection screen...

make sure you have the same settings:

Check "Loop (Restart when wav ends)"
Check "Stretch Tempo"
Tempo - 100 (this is the tempo of the loop - which is 100 - not the song you are using it in)
# beats - 4 (again, meaning in the loop used)