Yeah, usually this ends up happening by some kind of corruption. There are a couple ways to prevent this:1.
Make sure you're using the dual-boot installer booboo released in mid September. It was made to solve write errors that cause corruption (I lost a good 8GB microSDHC card because of such errors forcing me to reformat multiple times). You can get it here2.
Always safely remove/unmount your MicroSDHC card when writing to it. This should be obvious I guess. In linux, not unmounting is a huge issue. From what I understand, files you copy to a removable drive in linux is written to a cache, and is then written when you unmount the disk. So, unmounting is a big deal.3.
Avoid using SELECT+START+POWER to restart your Dingoo when in linux. Doing this is like pressing the reset button on your computer - it causes seriously problems for your hard drive (and in this case, your microSDHC card).
Those are my tips. If anybody else has any, please let us know!