My FS-100 (v4.0.0.04080107) is suffering under the same symptoms. We went to transfer video from an event we recorded, which should have been an hour, but all we found were several clips, two 1 minute and one 22 seconds.
There were other oddities, such as the two drive icons in the Finder not both being the yellow Firewire drive I was used to seeing. So I decided to Repair Disk and Format to see if that would clear things up. The drives do now look normal in the Finder, but I made several test recordings, and they all freeze early on, even though the file continues to “play”.
My observation was that the counter stopped during record, even though the recorder continued. I had read elsewhere about someone having trouble with their Firewire connection and thought that maybe an intermittent connection would be to blame. I changed cables, but that didn’t solve it. – Paul