Sorry to be butting in here, but just like to confirm you have tried shutting the virtual machine down and restarting it? We had a similar issue and the only way we found to resolve it was to power off the vm.

Before people mention that the application was not multi threaded, in our case it was a single vCPU machine and even running cpubusy.vbs would not take us over 50%... shutdown, power on... 100% CPU.... wierd I know and have not seen it again.

Kind regards.