Every once in a while q3map2 will choke on a surface or two and bork the coordinates completely. It tends to do this after the the vis stage(somehow), which means it won't leak, and you never know it happened until you test the map after a complete compile. The best way to fix the problem(which will recur every time you compile) is to just delete the brush and remake it in GtkRadiant.
The fact that you have to remake the brush probably suggests that it is a bug in GtkRadiant, not q3map2 or Tremulous. GtkRadiant might be outputting the wrong data into the .map for the brush, but it still parses OK for GtkRadiant(since it doesn't need to know much besides the coordinates for the brush, and the texture on the sides). Fixing the .map by hand is probably impossible unless you know how to read a .map file.