Like this thread here...
http://www.lackeyccg.com/forum/index.php?topic=1726.msg13260
I've run in to this problem after creating my own plugins (and it also exists in the Munchkin plugin) when right clicking cards loaded to the shared deck. I attempt to right click cards from the SHARED DECKS and "SEND to Top of" OR "Send to Bottom of" any area, the cards instead disappear in to the ether and are just gone. Dragging the cards to the destination areas works just fine though.
Is there something I'm missing? I'm willing to post code to anyone willing to look... But everything else works EXCEPT this.