I ran into this while testing my mod manager for BZ98 Redux and BZCC (currently in beta version 0.1.1.0).

For some reason, if a multiplayer server has more than one mod active (as in the config mod has dependencies on asset type mods) the GOG user cannot join the server and is always rejected indicating the mod is not installed. Interestingly, if the mod is only a single config mod and does not use asset type sub-mods the GOG user can join without issue.

In all these cases I have confirmed the gogworkshop folder has the up to date mods installed and set up correctly.

An example of a mod showing this behavior is my own Reactor Wars. "Reactor Wars" [1364727893] has dependencies on "Nielk1's Lua API Wrapper" [1364723281] and "Expanded Stock-like World Props" [1364724970].

I believe the cause of this issue is the logic which, on the Steam version, downloads dependencies when the mod is activated from the mod menu or when joining a modded game. Because the GOG version does not have this logic, it is rejecting outright instead of checking if all the mods are installed.

I've posted this here to be sure the devs see it, though I am also bringing it up internally with what contacts I have.