This is one of the big problems i have found (and has prompted a switch, well, if it works, to native linux) - i have found that VMs require a lot more babysitting! You need to open up the task mananger and click the 'show all processes' button (log in as admin etc if on vista). You then need to change the priority of either one of the VMware clients ot of the gfx clients. I do both to make sure - right click on 'VMware-vmx.exe' (something like that - it has vmx in the name!), choose change priority and set it to low. Do the same for the Fah_core_11 processes and set their priority to high.
You could also change the affinities of the processes - that way your VMs will execute as fast as possible. Assign one VM to two cores only - do this by right clicking on the process and choosing set affinity, then assign it to cores 1/2, 3/4 etc. Do the same for the other, but choose the other two cpus. I would then assign all my commonly used processes to one set of cores (eg opera/outlook/winamp to cores 1 and 2). You can then set one VM process to 'low' priority and leave the other at normal (or even set it to 'above normal') and still use the pc (things get a little slow otherwise). This is not really necessary - more of a personal preference since i use the pc whilst folding. Experiment with the prioirties and see what sort of difference it makes, but it does require some looking after.
There are programs available that will automatically switch priorities for you. SetAffinity2 will let you set affiinities and change priorities (i think), but ididnt really get on with it - easier just to do it manually since i am always sat at the PC. Unfortunately there is not easy way to get around this. You can change the priorities in the client config (runnng the -configonly flag), setting the smps to idle and the gfx to low, but im not sure this will solve the problem.
