Running flshell could be the problem but I don't know. It's possible but since I was on vacation when the flshell news was posted and it is not hosted here on Lancers Reactor, why it's not hosted here I couldn't tell you. I didn't bother finding out about how it works.
Maybe Chips knows something about flshell he was the one that posted the news about it.
Good luck finding any information on the flshell website because it seems to be offline... at least it was when I checked
http://www.skif.be/
The fourms seem to be offline also
http://www.skif.be/forum/viewforum.php?f=1
The only thing I found on flshell was the news post here on Lancers Reactor
http://www.lancersreactor.com/t/news/newsitem.asp?id=3479&category=Freelancer and the news post does not mention dual processors or dual core processors.
And you're talking about running a server probably with IONCROSS too which is different than just running Freelancer on your computer. Unless of coarse you're playing Multiplayer, in that case you have to start flserver.exe first in order to connect to your own server in Multiplayer mode.