A couple of questions

[Ualaa]

Not sure what your system is like now.
Or what your budget would be for upgrading, if you decide to.

I'd suggest posting on the forums at www.isboxer.com
Lax would have the best chance at figuring out your issue.

I've got my slave windows limited to 20 FPS and the main to 60 FPS.
Fef had a post within the last few weeks, where IS Boxer would lower the settings on a slave toon and raise them on the master toon.
So, my video settings are very low for all of the slaves (4 toons, on each team), but are at moderate levels for everything else except maximum on view distance for the master of each team; and when I switch characters, the high/low settings are applied.
Low settings on the slaves, especially shadows and view distance can help out a lot too.

I'm running with each of the physical cores, on all game clients.
And none of my logical cores assigned anywhere.
Not assigning the logical cores, was a very slight performance boost for me.

[Lanky]

Not sure what your system is like now.
Or what your budget would be for upgrading, if you decide to.

I mentioned a rough hardware in the first post, I can get a more detailed one when I get home.

Nvidia 8800GTS
8G ram
Dual Core 2.5ish Ghz machine

I currently have all the graphics turned down except for the view distance on my main character. I put my main on 1 cpu and the other 4 characters on the other cpu. Might put all my characters back on both cpus and see what that does. When I changed the cpu affinity originally I was tweaking a few things....should probably see if that 1 change is making it better or worse.

As for budget, I normally spend ages convincing myself to spend the money on an upgrade, but once I do it I am normally happy to spend a bit of money and do it right, so I would probably get a nice i7 950 with a ATI 6870....