I am not having the sd card issues, but if an app is beating the card to death with constant writes, it could happen. That or an odd power spike- or connection issue that eventually shorts the card out.
Seems this could be related to the motherboard issue and why some have the problem and others do not. My 64gb is filled up with tunes and game roms and has worked fine since the GS3 launched.
I have a VZW 32GB blue.
As far as files not always being seen, that is a normal problem with MTP and I run into it with all my Android devices that use it. Unplugging and replugging the device and giving it a minute to index usually fixes the issue. MTP sucks.
That all said, if it were a write issue, seems all the devices with apps2sd would have had the problem too. I do not recall a focus on the issue in the old days of small internal storage devices.