I have the same modchip and same problem. What i tried is the USA version. I burned the iso 1:1 without any patching. When i try to load the game from the channel it tries to read the disc and brings me back to the system menu. I tried the patched iso too - when i put the disc in, it doesn't even show in channels - it goes straight to a black screen with the error message. I tried putting the HBC without changing any system files, just the HBC and neogamma r8 beta 12. When i load the game through neogamma it shows a green screen and takes me back to system menu. BTW - i installed the updates that come with the game - it updates the system menu to 4.1u. I don't see any side effects - i still can play backup discs of any region.
A friend of mine told me that he made it running by installing the updates from an ORIGINAL copy of NSMB and then he was able to play the backup disc without any problems. My original copy is coming this week and i will try that too
As for now i hope the modchip producers will come up with an update to their firmwares - that is if they want to stay in business