One big question: Did you change the power profiles at all or attempt to overclock with the new kernel? (If not, why did you install it?)

One thing that's a known possibility with under-volting is corruption happening when writing to flash memory. It was first seen back when Titan was playing with voltage curves. While most devices won't have a problem with it, some marginal devices may still see it with the lower voltage settings. So, if you did set it to low voltage, or set the overclock to max, that may be partially to blame.

It could also be that you just have a corrupt block in your flash memory. That happens sometimes. Your best bet for that is to reformat the flash memory and use a tool that does a simple read/write/compare to find/map bad blocks.

If you want to recover files, your best bet is to use one that scans the raw device looking for blocks that used to be part of the file system. R-Fat did that, as does foremost. It looks for disconnected directory entry tables, magic values near the head of a block, etc. It can sometimes find files that were completely lost due to corruption.