When I play a sample in Polyphone it loops fine, but when I insert it into an instrument it clonks at the loop point when a note is held. Not all the samples for the instrument do this - most loop fine in the instrument, but I have three that clonk. When I play that instrument outside of Polyphone any notes using any of those three samples don't loop at all.
There is no reason for such a situation to occur.
If you have selected the correct loop in the "instrument" section and the loop points are correct in the sample section, there is no problem.
Note that there are no numbers entered in the "start loop offset" and "end loop offset" sections at the bottom of the page in the instrument section.
Also, any values in "sample star offset" and "sample end offset" should not be crossing with loop points.
The offsets all appeared to be OK, so in the end I started again with a completely new soundfont and re-created the instrument from scratch. It all worked OK then. Sometimes that approach is quicker!