Using Lion, my trackpad settings got all scrambled about a week ago. Initially I thought they had reset to defaults, but when I looked at the preferences, it was just a bunch of randomly selected choices.
Anyway, you probably just need to go into the trackpad preferences and reset your options. In System Prefs -> Trackpad -> Point & Click, there's an option for "Secondary Click." (re-)Check that and then, beneath it you can choose, "Click or tap with two fingers."
Oops sorry. If you're certain the option is still on and set correctly, maybe there's an issue with the trackpad or its software. Do other multi-touch functions still work? If yes (or no, even), have you tried to universal fix of rebooting?