Neogamma is garbage for DML. It was good 16 months ago, but hasn't really been updated since. Which revision of USB Loader GX? "3.0" is also pretty old, there has been various beta "r" versions to enable the newer DM/DML features.
For SD card, FAT32 with 64k clusters should work (and was recommended at one time, not sure if that is still the case). For USB, 32k clusters are required.
I have links to three USB Loaders in my signature that all should work with the latest version of DM/DML.