Not sure what`s going on, but I linked to my textures folder in baseq2 (baseq2/textures) and it doesn`t load anything. Looks like a great program tho. I plan to add some Q2 mapping in the mix to my Q3 mapping and this will be useful for overrides.
Edit: an issue was found with spaces in directories. c:\quake 2\baseq2\ or c:\my games\quake2\baseq2, could this be what is happening on your end?