I guess there are two different types of FPS you could measure. You could run a game that shows its FPS, but that just indicates how frequently it's able to update the virtual screen, which I assume is not what you're after. I assume what you want is actually a measure of how often the hypervisor - or whatever you want to call the software running on the host - updates the VM's window from the virtual screen?

If you don't need the FPS number specifically and just want to know the overall performance of the VM, you could run some common benchmarks like 3DMark1999, 2000, 2001, Cinebench, AquaMark, Phil's DOS benchmark pack, etc.

My first suggestion would have also been Fraps but I don't use it enough to know a workaround the problem you're experiencing with it.

Lastly, if you're not set on using a regular VM and can use 86Box instead (hardware emulator), it expresses the current emulator speed as a percent, so if it's at 100%, you will know it is emulating whichever system at 100% of its nominal speed on the host hardware.