Try running both instances on core 0 then and see what happens. From what I have heard, it doesn't work right on core 1 for some reason. I just suggested to try that as a troubleshooting step.
If I was you, I would stop using all of the programs for setting affinity and just change your shortcut to start EQ with the /SETAFFINITY 0 command. I am not 100% sure that is the command, but I have seen posts somewhere on these forums recently where people have used it. I think they give a good example if you can find that post.
I know I have heard that sometimes those programs will work and sometimes they just won't. It sounds like they aren't working for you, so you should try it without them if you can.
Found the post I was thinking of. Check the batch file that So_Leet made here:
http://www.eqemulator.net/forums/sho...light=affinity