look in the mapper2.cfg file to see if it is pointing to the fallout 2 directory and more specifically to the master.dat and the critter.dat.
these do not need to be unpacked, but they can be..
then check that the master.dat and critter.dat is in the fallout 2 directory and that they are named correctly.
if you chose the small install then the master.dat is read from the cd.. if you do not have the cd in then the editor will not be able to read the dat.. ( duh!! )
before using the editor do a FULL install of fallout 2. THEN re-install the editor.. use the default paths for each ( ie don't specify a different folder or drive.. )