I see from this thread that you are experimenting with the sdhost driver - if this is active when you are seeing these problems that it is most likely your cause. If so please go back to a fresh install of RC3 (not RC2) without this test kernel and see if you are still having problems.
The Evo 16Gb cards are known to be problematic on Pi 2’s and up until RC3 were experiencing data corruption issues that could lead to all sorts of weird and random problems.