I have recently started using sub web's which alway's open a fresh instance of FP for the new web. This means I have two copies running, but technically this is NOT what your asking.
I have in the past had dual boot systems & the configuration I used was Win98 on C drive, win2k on the D drive with programs being installed on an E drive. I tried this and successfully installed office into the same directory on the E drive for both OS's and it worked successfully. In your case though I think you would have to ensure FP had seperate folder of each version you wanted to run.
Hope this helps