Ran chkdsk /R /F from command prompt, and it found no errors. I also ran "error checking" (right click on drive, properties, tools, "error checking"). It, too, found no issues.
FYI flash is not like a hard drive and bad flash sectors are usually automatically remapped in the cf card's firmware so unless it's totally screwed a chkdsk /f /r /x won't help or let you know there's a problem. It's technically possible that it's still the card but i'd still suspect some camera bugs.