I ran into a similar issue as well, although I was trying to copy/paste two KCMs to a new PRT loader, it pasted two KCMs but they were a duplicate of the first KCM (the bottom most KCM in the stack) instead instead of a direct copy.
Found the culprit.
In the on Clone event handler, the last function call ensures any exposed parameters are reexposed in the KCM_CA custom attribute.
This causes the Modifier Panel to change focus and move to the top modifier, which confuses the “this” context and the wrong modifier gets updated in the next event handler.
A quick fix would be to remark the line
–KrakatoaChannelsEditor_Functions.exposeControlsToModifier this
in the end of the file “Krakatoa_PRTChannel_Modifier.ms”
This will cause Exposed parameters not to update automatically after a copy operation, but you have a way to update them manually in the MagmaFlow Expose menu.
A better solution will require some more work as I have to figure out how to update the CAs without losing focus.