I'm having a similar problem, Once I've set protection on an article I am unable to remove it.
I've tried updating the bitfields, I even tried the direct link:
/admincp/index.php?do=buildbitfields
But the results are the same - even after a refresh of the page, or trying protection on a new article.
The page tells me that the new protection has been completed but when I go back to the article it has remained the same as I initially set it.