Make sure that you have the files properly named. Freedoom should be doomf.wad and doom shareware should be doom1.wad. If you pick the wrong version of doom for the addon you will see those types of problems. Rockdoom picks the version of doom it thinks is running based on the main doom WAD you choose. If you pick the wrong one it will be looking for the wrong files within the WAD. Same goes if you mismatch an addon with the wrong version of doom.