I'm havingan issue where the payment gateways are missing. I have MarketPress activated on a single site of my network. I only see "General", "Presentation", "Shortcodes" and "Importers".
Even when the plugin was network activated and gateways enabled from the network admin dashboard, these were the only few options i had on my subsites.
I did try using the TwentyTwelve theme and deactivating all other plugins, all with no change.