If get the message that your meshes don't match when you try to join a mutiplayer game ("Your mesh files differ from the host"), you may need to uninstall, delete your Sins folder entirely (do this manually!) and reinstall.

A quicker alternative that may work in *some* cases is to just delete the following files from your regular Sins Mesh folder (not the Entrenchment Mesh folder).

SupportShip_PsiGunship.mesh
SupportShip_PsiDecoyFighter.mesh
SupportShip_PhaseGunship.mesh

These are located in something like the following:

C:\Program Files\Stardock Games\Sins of a Solar Empire\Mesh