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Make sure to change the expansions from "-game hipnotic" and "-game rogue" to just "-hipnotic" and "-rogue" in the DOSBox conf files or the command line, otherwise the expansion's huds will not display the correct graphics and info.

Just thought I'd put this in the Quake subforum as well until (or if) GOG fixes it.
Good catch!
This fixed yet? Or do you still have to do it yourself? :P
Tried to follow the instructions in the first post, but the HUDs didn't seem to change...

Which file exactly do I need to manipulate? And how do I see if it works?