It must not be the CF card then. It started doing this not very long after I built the system, so it's probably not write cycles anyway. I suppose it could be that some hardware was bad out of the box, but it was working fine at first, so I don't know.
@cmb:
if it were the CF you'd be seeing at least some errors in the logs, and usually a ton of them. Write errors, timeouts, something on adX or daX depending on what your CF device is.