Well, I'm looking at those corresponding files on my machine and nothing in those directories is being changed by root on a regular basis. The way they're set up now, only root can change them. I suppose all those files were changed to mode 777 and all the data, save the filenames, destroyed by root on Sept 25, at 5:39 and 3 minutes after at 5:42. The timing somehow makes me think it's a shutdown realted issue... My question would be what could root have possibly done, or wanted to do that caused that? It can't have happened too many days after you installed beta, so is it right to assume that the rest of us have a time bomb on our machines that's about to kill our terminals and all those commands as well? I want to think of some preventative action to take.
I noticed root did change my ssh prng_seed file mode to 750, and ssh wanted it to be at 600. I don't know what caused that either.