This sort of thing happens alot
if your files aren't identical all multiplayer games freak out.
One thing to keep in mind is alway remember which order you apply mods and deactivate them in the same order.
Trying to fly in a ship that doesn't exist doesn't help (been there)
Setup whatever mods you want then copy the "freelancer\data"to your mates computers (saved games are held safe n sound in "my documents"
I heavily moded New York then discovered that no one in multiplayer could dock with out a damned "do you wish to report your incompitence to microsoft" box turning up. Once I got rid of a few things (gates, lanes, planets etc) it worked again.
If you apply a mod make sure it works in singleplayer (mission 3 flaged up problems in NY)
It's gonna be either a difference in files or a mod critter stuck in the pipes.
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having infiltrated so many government installations I am now availble in your local store