I think it might be the latter, and either the other partition is corrupt or wrongly sized.
As I know people have tried to obtain root access in order to try and side load apps, and failed. So that would suggest that the OS section at least is locked out. So either there are 3 partitions (OS, Pre-installed apps, everything else) or just 2 that are separated by privileges; which I suspect is the easier option to do on bulk.
Perhaps it is something to do with partition size, as some people have reported that the available space fluctuates following resets, etc.
As it isn't effecting everybody, then it would suggest it is component based rather than firmware. Otherwise everyone would have it. It might also suggest why it is taking Samsung so long to fix, as they either need to go and replace all the HDDs (not really an option), do a recall (expensive) or roll out an update that re-formats the partitions (best option).
But they would need a way to detect who had a bad drive, or risk formatting the partitions of people who are unaffected; I also assume that it would lock the TV out of operation for a while, as the processor would be tasked by the formatting process.
Of course, I could be barking up the wrong tree, but the theory fits.