Yeah, the rumble patcher sucks. Try it with different games, it will probably work with some of them.
Another thing you can try is to patch a game that's very small after trimming (like Elf Bowling, or that Japanese match stick puzzle game), then start that game, soft reset out, and start the game you want to use rumble with. (the N-Card clones have soft reset now, don't they?)
That way you only have to patch one game, and you avoid the possibility of the rumble patcher causing the games to crash/glitch out.