Weird. I'm pretty sure everything is set up correctly. I'll try with New Super Mario Bros. myself. Currently my testing is limited to two Castlevania games and Kirby.
On a side note, AMAZING work to the people behind this. The stuttering that kept me from using TWLoader is all but gone with this new thing!
EDIT: New Super Mario Bros. is fine. I'm not sure why stand by would force close the loader on other games, but stranger things have happened. According to the compatibility list, it SHOULD work though. Can you confirm that Order of Ecclesia and Kirby Squeak Squad both cause the above issue?