MarketPress custom shipping plugin in theme not showing all admin options

Howdy,

I modified the flat-rate shipping plugin and want to include it in the theme I'm developing, rather than dropping it into the plugins directory in MP where it'll get wiped out every time the plugin gets updated.

I include_once'd the php file with the class and the appropriate mp_register_shipping_plugin from within my theme's functions.php and I get the shipping option in the drop down in the admin area, but the shipping_settings_box and shipping_metabox aren't showing up.

I even tried moving the mp-flat-rate.php to my theme directory (from the MP plugins dir) and it is doing the same thing -- shows in the list, no meta boxes when selected. Any hints what's going on with this?

What is the proper way to include shipping/gateway plugins from my theme to keep them from getting wiped out by MP upgrades?
Or should I make it another plugin rather than include it in my theme?

Thanks.