You have to be more specific about your situation. Here's some info you could provide that would help us figure out your problem:
1. Current firmware
2. emuNAND or sysNAND, with or without A9LH
3. Source of games (eShop, freeShop, CIAngel, that iso site, physical cart, etc.)
And any other information that may be pertinent to your situation or specific 3ds.
sounds like a dodgy sd card.... you might be reaching the bad sectors or fake area of the sd card with the last (new latest) games you installed. so the system probably written bits of the installation on bad parts of the dodgy sd card you have..... that's my theory anyway