NDI, I think you are using the old, 0.3x version. You should upgrade to the latest nightly of -this- version(just download and extract the .tar.gz), which will also overwrite the old version.
This version has no specific "checksum" function - It's not easily possible. Unlike the old version, this one works with files, so each file would need to be checksummed and compared - a non-trivial task.
It -should- work right though, as the UbiFS filesystem is error-correcting, and so should prevent disk errors etc.
The old version was -not- aware of bad blocks, and so could easily write into a bad-block, creating corrupted data randomly(specific to each N900). This is probably the problem with your system; you ended up with a bad block in some specific file.

Helmuth: I'll look at the read-only/read-write; I'm not sure entirely how to make it Do The Right Thing(TM).