This is due to the molecule not being read into vmd upon startup (at the time of your .vmdrc file being read). I suspect you start vmd from command line with "vmd molecule.file" rather than opening up vmd first, then loading in the molecule from the File > New Molecule tab. If you do it the former way, then your "mol" instructions in the .vmdrc file are being applied to a non-existent molecule. The latter should work with the commands you've provided.
See here for how to get these defaults working for you with a command line startup.