also, I haven't tried re-downloading or re-installing yet.  

I have also had this happen twice. Whenever it occurs, I restart the game and everything is fine again. I am unsure of what causes it, and don't remember what I was doing prior to it occurring. honestly, I've also put maby 30 hours into beta5 as well and it is very rare.

I don't think a reinstall deletes the folders in your documents, where all your custom units are stored.

For example this headless problem only occured when I restared a game after loading one.  (From which I learned is a big no-no right now as they are not clearing stuff when you quit a game yet).

When this happens does it happen after a reload or something like this? You should also check to see what custom units are in your folders as I think a problem might lie in the reading large amounts of characters in there. (I can get this glitch with as little as 5 sovereigns in the reload). I don't make any custom units, so I guess I haven't been able to check this out that way.

I will try to make lots of custom units and see if I can get this equipmentless (empty) character problem and see if that does it. This bug has me curious.

It happens in both new games and loaded saves.  Yesterday it happened at the new game screen.  I have 17 units in my units folder, I only deleted one duplicate sov file, but it's only happened once since then.