Hey samofishfire,
the uforadiant coming with the installers of 2.4 and 2.5-dev is broken. There are several threads about working solutions in the Mapping section, like
this one and
this one.
If I got you right, you already have a working copy, but it´s not in the game dir? You could try and a) remove the broken radiant version from the game folder and b) copy your working one in there.
As already said, radiant should be able to read the .pk3, but maybe it isnt. You should extract all of them and remove the .pk3 afterwards.
Iirc the radiant from the download page was working last time I tried. What os are you using? What game version?