Interesting
I have been bitten by the firefox behaviour to spawn another thread from the existing firefox session rather than open a new instance. But I am confused as to how this behaviour you describe is even possible across local and remote machines. I just had to try it and you are right.
If for example I launch my local copy of firefox and then ssh -XC over to a machine at my office and launch a copy of firefox from there I get the usual delay I would expect with X forwarding a hungry app over ssh and DSL and then as you say and contrary to what I expected another instance of my local version of firefox pops up.
Fortunately there seems to be a cure
Allegedly setting the environment variable MOZ_NO_REMOTE to 1 on the remote machine before launching firefox will fix it
Further to that on firefox 2 you can simply add the option when launching the remote instance i.e 'firefox -no-remote'