Just to back up ace671..
My friend and I are computer technicians, so obviously as techies we decided to find a way round the issue rather than uninstall the game which takes time to then reinstall the game taking even more time.
The solution was quite easy for us.
Get one of your friends to go to C:\Program Files\Kalypso\Sins of a Solar Empire\
C:\Program Files (x86)\Kalypso\Sins of a Solar Empire\
if you are running 64bit.
Get him to Copy the folder called "Mesh" and then get him to send you that file via email, network share, whatever, you just need that folder.
Once you have it, find your own Mesh file and take a backup of it and put that somewhere safe. Now import your friends mesh folder into the same location on your machine, replacing your previous one.
There is now, quite literally, not a single chance that the error can say they don't match as you have an identical copy of each others.
The games work fine, all the expansions work fine, previous game saves work fine. It just works.
This fix has been performed on a selection of operating systems ranging from Windows XP, Vista, Win7 (x86 & x64)
This solved the issue for us and we can still do online games with other random people on the internet, so yeh, simple copy and paste saved us from the need to uninstall the game on everyone's computer because it was impossible to say who's computer had a dodgey install in the first place.
Ace beat me to it, but this post was designed to make those realise that this fix works on a variety of operating systems including different architectures.