coinheaven, does the cart you're testing on have SRAM and if so, how much. For complex technical reasons, the cart needs 8k of SRAM to load the level data to. While we don't use it for anything other than extra ram (i.e. we don't actually use it for game saves), it would be sure to not work without it.
Come to think of it, how common are MMC1 carts with at least 4 banks of PRG and 8k of SRAM? At the time, I didn't really worry about this issue as I've done all my work on emulators (my NES hardly works, so I haven't bothered getting/building any flash carts). I mean, I've got one (not flash modded), but it's an original Final Fantasy, I wouldn't want anyone to use one of those for a doner cart.
I suppose I should put exactly what is required of the cart in the README, although, IIRC, it's all in the header anyway.