@clicker, I also have never had this issue. You mention using passwd to try to resolve it. I wonder if you might have used passwd before and that that is the cause of the issue in the first place.
The only thing I would like to add to what @Moem said is: First reflash without ticking the wipe option. (In fact, I would leave all the options unticked) If that doesn't fix it (which I suspect it won't) then you will unfortunately have to backup the data you care about, flash with (only) the wipe option ticked, and then restore the data.
