My friend has a DSTWO card, and it works fine on my system. I put her Micro SD card in my DSTWO, and nothing...meaning, it doesn't show the "Stormbreaker" game in the first slot. It just doesn't detect the card at all.
I wish I could find the email receipt...I've looked...I don't know if I deleted it or what :-( Awesome job, I know lol
If your mem card works on your PC, then make sure your games and saves are backed up, format your card, got to http://eng.supercard.sc/manual/dstwo/download.htm
Download Firmware_v1.13_eng.zip, go into the En folder, and drag dstwo update to the root of your mem card. rename the file with -b at the end.
Next download DSTwo latest patch at the top of the page, go into the en folder, and put the _dstwo folder in your root.
Lastly, download the EOS files, go into the DSTWO_v.1.11_1108_engfolder, and drag _dstwo folder and ds2 boot.
This is all just to be thorough...
Next securely put your micro SD in your DSTwo, and run it on your 3DS, wait atleast 2 minutes, and restart, if you're still getting nothing, then perhaps there are two things going on, a defect is happening thats not allowing mem card access, or the unit is broke by something else. Both will need a replacement.