Well, sorry, but the other topic was related to textures, but anyway.
Here is what i did to solve this
I made autogen.cfg 777 and made sure i owned it.
I did that in 2 places, somehow i have 2 of those files one in ~/.tremulous/base one in ~/.tremulous/base2
then i opened ~/.tremulous/base and changed some options to look like this:
seta r_customheight "1200"
seta r_customwidth "1600"
seta r_fullscreen "1"
seta r_mode "-1"
and now it works.
thanks