I had a very similar thing happen to me just yesterday. I had freshly installed 1.3.11sr1 on about my 8th site, and everything seemed to be working fine, when suddenly it started giving me an error message when I tried to add or edit any but the original ("Welcome to Geeklog"
story. I had successfully added a new story just minutes before, but then when I tried to edit it I got an (apache, from the look of it) error page which told me I did not have permission to access /admin/story.php. This happened over and over again, no matter what kind of change I tried to make.
It turned out that I could delete the new story, but could not do anything else with it, in either plain text or HTML mode, nor could I add any new stories after that. Oddly enough, I could still edit the original story at will.
I had to go to work at that point, so I did nothing. When I returned home some hours later, everything had apparently returned to normal and I could once again add and edit stories normally. So I wonder: what was the problem?