I am using wordpress as a CMS, and currently have 3500+ categories... There are 30ish top-level categories, each with a number of 2nd level categories, each with a number of 3rd level categories... when I add additional 3rd level categories, often they don't show up in admin>manage>categories or on the site itself, though they are in MySQL, I am not using any caching plugin, and have installed and run the flush-cache plugin<br>
Sometimes it takes a few minutes, hours, or days for the 3rd level categories to show up.<br>It's not my browser cache, there's no system cache that I know of on the server, and I don't have any caching plugins.<br>