First I want to mention I tried this on two different computers with the same results. Easy 3.2.1
Step 1 - rearranged the desktop icons manually by dragging them to different locations and also tried to align them as neatly as I could. There does not seem to be an underlaying grid that lets me snap the icons to.
Step 2 - saved this arrangement as custom profile (JWMdesk > Icon Layout) and hit apply, which retarted X as expected. Which after being back to a running desktop had changed the arrangement, to be precise the LockScreen icon was moved to the right side of the screen. Everything else was still at the same location.
Step 3 - I opened the "custompin" file and manually changed the x/y coordinates of the icons, first of all to get a better alignment and second of all to place the LockScreen icon back into position. After restarting X from the menu, everything was back to the same less aligned arrangement and the LockScreen icon jumped back to the right side of the screen. After opening "custompin" again, I noticed the x/y values were still good, meaning the values I entered manually, were still in place.
So I went ahead and opened the PuppyPin file to compare it to the custompin file ... and it was different, reflecting what I had on the screen. Also noticed the order the icons were listed in the file was different from the custompin. Not sure if this makes a difference as long as the coordinate values do not change? I don't think so.
Not sure what's happening there, or if other users experienced the same, or do not have problems with it at all. And like I said, I tried this on two different computers with the same results.