Are you sure the map is being launched with your mod being selected via -game your_mod_name? Can you make some other change in the mod that will be really obvious, like setting starting health to 200?

If the command line for the mod is correct but the mod still isn't loading, run the checklist to be sure is that your progs.dat file is being used. Make sure that it's in the root directory of your mod, and that there are no .pak files in the mod directory which also have progs.dat in them (files in a pak will take priority over unpacked files).