I've used FATFS on STM32 before successfully under ChibiOS. Make sure your disks are formatted correctly. E.g., format them on a Windows machine to be sure. I think there's a format routine in FATFS itself, and that works too.
Does your board have a FET or some way to power cycle the card? If so, make sure the card is getting power (duh!). I noticed that when the cards boot they'll often suck down a big gulp of current. If you see that pulse, it probably means the card is working. However, you'll want to make sure that the rest of the system isn't browning out somehow.