Multiple rdpthread.exe Processes Using 100% CPU

I can't answer the question, but I can add an extra little bit of anecdotal evidence. I have noticed this too, with a Linux hosts (Debian/Etch and Debian/Lenny).

After some mucking around when I first noticed the issue, I came to the conclusion that the issue is VMWare, not the guests themselves. Upon stopping all services in the VMs on a particular machine the CPU use remained high despite the OSs in the VMs doing nothing. On shutting down each of the four VMs the excessive host CPU use dropped by about 25% per VM (I didn't measure this by any scientific means, but certainly no one VM seems to be imposing most of the load). After restrting the VMs the CPU use remained where it used to be, even with the services in the VMs active, and the load has begun to slowly rise over time with no related rise in apparent useful activity.

In both the cases that I have noticed this happen, the host OS has been 32-bit Linux and the guest OSs have also been 32 bit Linux.

I have not seen it in all cases though. On my home server (64 bit Linux kernel with 32-bit user-land running one large and two small 32-bit Linux VMS and occasionally Windows VMS for testing) and the main dev/test host at work (64-bit Linux (both kernel and userland) host running mainly Windows VMs, some 32-bit and some 64) this aberrant behaviour doesn't seem to be present. All the above are running VMWare Server 2.

So to cut a long story short: it isn't just you, and it isn't just Windows based guests, but it doesn't seem to be a consistent problem (as many arrangements don't see it as do, in my limited experience). Though unfortunately I can't help any further than that as I've not had the time to look into the problem in more detail.

It is natural that when you remove one bottleneck (disk IO), the system will speed up to the point of hitting another bottleneck (in this case, apparently, CPU). You should improve the efficiency of your code (so that it utilises a single core better), parallelise your code (so that it can utilise multiple cores simultaneously), obtain better CPUs, or learn to live with it. Is your site running slower than is acceptable for your situation?