EQ and EQ2 are two different games. I have never had a problem as the OP stated with EQ2. I had it all the time in EQ. Multiplicity still locks up the primary computer in Everquest. I seriously doubt this will get fixed. Everquest works differently then EQ2 and WoW, lots of boxer type programs do not work well with EQ and it's because of how EQ handles inputs as backgroud/foreground. There is a program called Innerspace that will force EQ into the foreground where inputs will work and I assume multiplicity will work, but I never tried it. I just use my ultraportable laptop as the primary machine and have EQ on other machines. So long as EQ is not being played on the primary machine, all is good.
Also, I 6 boxed EQ2 for a bit using mulitplicity and had it all running in full-screen. Worked fine.