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I was helping @JohnAguiar out with some WordPress issues a few days ago and lost quite a bit of my lunch break going through trying to solve his problems which may have been related to a single plugin.
The problem was first that his last 2 posts weren’t showing up in his Feedburner RSS feed, this put is on a goose chase where we did everything from troubleshooting Feedburner itself, 512k max size feed being blown, a feedburner plugin, to finally narrowing it down to W3 Total Cache which was caching the RSS feed.
In doing all of this troubleshooting we also updated his WordPress to 3.4.1 and all plugins. This didn’t resolve it but when I disabled W3 Total Cache, problem went away, this narrowed it down but another problem surfaced.
Now his last 2 articles were not showing up on his homepage, but did on his RSS feed. This one blew me away, it took me quite a while and I attributed it also to W3 Total Cache at first (must be cache not clearing) and I went through everything, then I read tickets online about theme and WordPress updates causing this issue so looked at that, switched to default theme for 1 second and it didn’t solve it.
Then Checked WordPress Plugins
Disabled all WordPress plugins and problem goes away, re-enabled plugins one at a time until when I enabled the WP Filter Post Category the problem immediately returned.
Learned more about the plugin and found out that John had created a new category a recent time ago and this plugin doesn’t automatically add new categories to it’s allow list, so this plugin was blocking any posts in this category from displaying on homepage and it was coincidence his most recent posts were in this category.
Always take a snapshot of all WordPress plugins that are enabled and then disable all plugins to see if problem goes away, there could be multiple problems at the same time but this is a sure way to rule out plugins really fast.