are you using the "auto add" feature of clonekey to add warcraft automatically when you load them? if so its bugged. it will add 1 warcraft, and acidently add somehthing else.

if thats not the case are you sure that you have "2" warcrafts listed in the "processes" window of clonekey? Make sure you have 2 of them in the program column, and in the process column the both have 2 seprate id tags. and the status on both are listed as broadcasting.

in my preferences for clonedkeys i have "only receive broadcasts from other subscribed programs" and "block standard WSADQE" checked off.