The function M-file lmp2cfg.m doesn't add the correct atom labels if the not all the atom ids are present in a dump file, e.g., the atom ids run from 1 to 3, but only the atom ids 1 and 3 happen to be present. The fix for this appears to be pretty simple: replace "aid = aid+1" on line 213 with "aid = atom_data(id(j+1,1,i),2,i)".
I'm not a matlab person, but I'll post the change.
Steve