Starting with WordPress 3.1.1, my previously discussed functions.php method for hiding posts filed in certain categories works again, and the latest workaround with RYO Category Visibility 3.0beta-9 is now broken.

There must have been a bug in WordPress 3.1 that prevented the former from working, which the latter worked around. Perhaps this:

WordPress 3.1.1: […] Fixes for various query and taxonomy edge cases that caused some plugin compatibility issues