I have a Yun whose SD card used to work (last week), and has now stopped working. I tried all kinds of stuff, including re-formatting.
Major symptom is this: When you plug in the card, it does not auto-mount and /mnt/sda1 is not found. ls can't find it. df can't find it. The format sketch reports that it can't find the card. Meanwhile, the SD card works perfectly in both a Linux Mint system and in a Windows 7 system.
I have been busting it for days, and have tried everything I can think of. I even bought another SD card. Same thing.
Possible problems: -some kind of crazy format lock-up issue (unlikely) -physical damage to the card connector (I can't see anything wrong) -electronic damage to the card connector, such as static or hot swap issues -corrupted drivers in /dev/sda
If nobody can tell me what is better, I am going to re-flash the Yun with the latest release of OpenWRT, but it would be much better to have an actual understanding of this problem (and how to fix it).
Thanks for answering this!