The issue here is with the change from 32 to 64 bit.
Multiplicity has a workaround for some games to stop them doing this which dates from a time when pretty much every game was 32 bit. This workaround does not impact 64 bit processes and the new everquest is 64 bit.
As you have seen an alternative solution is to take focus away from everything on the primary when controlling another computer, but this has its own set of consequences, especially for fullscreen exclusive games.
We are looking into the right solution and will update this thread once we have a plan in place.