I'm back guys. 13 days later and after looking around I haven't found anyone with the same issue as me. I'm beginning to think it's not my microSD but my CycloDS itself that is defective.
I might get another microSD tomorrow but I really don't want to waste my money.
As I said, everything works perfectly except for commercial ROMs (homebrew is fine). Other people are having this problem too but a simple firmware update seems to fix it for them. I have gone through 3 different firmwares (including the latest one) to try to get it to work. Another thing I've found is that my CycloDS won't boot properly if I have a blank microSD inserted. The only way to get it to boot with a blank one is to put another firmware on the card and force it to update using the recovery mode.
The card is perfect with everything else so far even though it's a generic brand. It has a really fast transfer rate (Class 6) and I have had no problem playing videos, music, etc. on it. I was even able to use the DS emulator on my PC to play the games I had saved on it without any lag.
I just want to know if I really should bother getting a new microSD or just return my CycloDS. I am reluctant to do either and would prefer to fix it myself because I don't want to waste my money then find that it still doesn't work, but I don't want to have to stuff around with the company I bought the CycloDS from because they are based in south Sydney and I am in north Brisbane. It's OVER NINE THOUSAAAAAAANNNND (divided by 9) kilometres away. And they will have to speak to the supplier, return it, check it, repair/replace it, send it back to the company, and finally send it back to me. All that won't be done until after the holidays are over, even if I send it back tomorrow.
If anyone has any suggestions that haven't already been made then please speak up because this is really pissing me off. This thing cost quite a bit of money and it won't even play games! I need something to do during for the summer holidays!