I’ve run into an error with the WordPress “Pages” system, having to do with child pages (pages with a “parent page” specified) messing up the list in the sidebar. Here is a verification of the issue, noted by someone else.
Oddly enough, it is only a problem if permalinks are enabled, which I just did today to try and get the unread comments plugin I was using to work correctly with Pages (rather than just posts).
My short term solution is to disable the page list in the sidebar, and (eventually) write my own plugin to do it the right way (at least until the WP devs fix it) or maybe even fix it in WP and submit the code.
I’ll also probably make my own version of the Unread Comments sidebar plugin, which is currently disabled since it wasn’t working correctly with the permalinks either.
At least my Recent Comments plugin is working with both posts and pages now. I realized I had to do that after getting a couple comments on the plugin page and not seeing them in the recent comments list.
Eureka! Turns out this was an already identified bug (934) and has been fixed by the WP team.
I implemented the fixes found in changeset 2421 and it seems to be working properly now.