You need both of these, beta5b is a update that disables patching of loaded .nds files.
Beta6 is in the works, with the loader reworked to use chishm's dldi patcher from his loader.
.SC.NDS loading only works on supercards currently, in beta6 i hope to get more cards usable thru the new DLMI interface I'm building.
A feature I want to have soon is the ability to flash gba carts from files on a slot1 card. Example: you have 4mbitcompo.gba on your r4, and your friend has a ezflash card, you can flash the .gba onto their card, and give it back to them.