This means gtkRadiant can find the textures, but q3map2 can not. It just assumes a default size (64x64?).
If you are using linux: q3map has (had, it should be fixed in SVN) a silly
bug that prevented it from finding textures in ~/.tremulous/base. I think it is looking in ~/.q3a and you can solve it by linking ~/.q3a to ~/.tremulous
I solved this by linking ~/.tremulous/base/textures to /opt/games/tremulous/base.
If you are using windows, this obviously won't work for you, but the problem should be the same: q3map2 can not find the textures your map needs, while gtkradiant and tremulous do. Move your textures to an appropriate location.
Read your compilation log.