In my situation, this is definitely a hardware issue...
I have two SGS 3s (one is 16GB and one is 32GB)... they are both running the exact same custom ROM and have the exact same SD Cards in them. One of them has now gone through three SD Cards... the other has not had a single problem.
I will be sending this thing back to Samsung immediately for a replacement. Perhaps I can ask them to upgrade as well in the process as I've read this seems to be an issue with the 16GB versions.