I think I know what the problem is. If you've ever been unable to DL a particular module, whatever the reason, Netloadmodule asks you if you'd like to select a different version/module to use instead. It then stores those in a file (NetLoadModule.ini). Mine has this line, for instance (among many others):

popup2=$litestepdir$modules\popup2-2.1.7.dll

I imagine that somewhere along the line you picked up an entry either deliberately or by accident that "reassigned" the module in question. I also assume that deleting all your modules made NetLoadModule scrap those assignments and start fresh. Rabidcow can probably confirm that.