I remember a while back I had FireFox 2 and FireFox 3 installed at the same time. Loading FF2 and then trying to open an instance of FF3 resulted in FF2 loading, and the same with FF3 already open and attempting to open FF2. The same may have also happened when I tried the stable FF releases and the nightly Shiretoko releases, regardless of the fact that they're installed into different folders.
I think you always have to close the instance of FireFox you're running to switch which version you're running. You may be able to rename the executable of one to something slightly different from default. Windows or FireFox may be looking to see if an instance of FireFoxâ€”firefox.exe, by defaultâ€”is already loaded in memory, and if so creates a new window from that loaded process. I cannot remember if doing this helped me out any or if I was just forced to close one entirely and open the other.