So I have found a bit of a silly solution... I just entered the games and saved in-game them directly on my 3DS. They have only been saved on my DSi before and I guess that caused an issue? After resaving each game on the 3DS they stared dumping normally. Strange, but as long as it works LOLI haven't had any issues dumping DS games on my 3DS... What game are you dumping?
Have you tried cleaning both the cartridge contacts and the ones in the console (with console powered off first) with isopropyl alcohol? Try that, then see if you get a good dump.
If that doesn't work, you might need to use a little paper to get the cartridge contacts to make contact with the ones in the console.