3DS endless loading screen, SD card malfunction?

I've been looking online for ages, but no one seems to have had this specific problem.

My (unmodded) 3DS is unable to open one cartridge game (ACNL, other cartridges I've tried are totally fine) and it's own, preinstalled apps like the Mii Plaza and I can only interrupt it's loading if I remove my SD card. Once removed, it can load eveything just fine, but cannot let me proceed to the actual games because the needed updates are on the SD card. Its definitely the SD card, since I've cleaned the ACNL cartridge and the inside of the console thoroughly before & made sure it's not damaged, the game also opened on a friend's console w/o issue.

I've got no knowledge of how to approach this issue, since I assume I'll have to manually do something with the files on my SD card, which I've never done before. I hope someone's got an idea of what to do.

Thanks in advance.