What ChaosX1022 says is correct. You don't have a bad/fake SD card. Sky3DS writes the game to the card in RAW format (that's what the format option does to the SD card) and doesn't allow fragmented files like a traditional file system (FAT/NTFS). Files are written sequentially and contiguously so for example (that's what the start/end sector means in diskwriter), if you had a 2GB card:
File 1 = 700mb
File 2 = 300mb
File 3 = 800mb
Free space = Approx. 200mb
If you delete File 2, you will have a total of 500mb free space however that 500mb is split between two chunks, the biggest file you can write will be in the 300mb space that File 2 used to take up.
To solve this, you will have to reformat the card and rewrite your games to it or run the optimiser option.