With almost 2.5M items http://commons.wikimedia.org/wiki/Category:Self-published_work is the biggest category at Commons. The category was hidden but vandalized in which the HIDDENCAT was removed. This edit was reverted (and full protection was added), but the category doesn't become hidden.
Query at the toolserver:
mysql> select * from category WHERE cat_title='Self-published_work' limit 1;
+--------+---------------------+-----------+-------------+-----------+------------+
cat_id | cat_title | cat_pages | cat_subcats | cat_files | cat_hidden |
+--------+---------------------+-----------+-------------+-----------+------------+
31 | Self-published_work | 2429973 | 26 | 2429892 | 0 | |
+--------+---------------------+-----------+-------------+-----------+------------+
So it looks like this row doesn't get updated (some timeout?).
As a workaround someone could set cat_hidden to 1. This would solve the problem for Commons.
Version: unspecified
Severity: major