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I am running into the exact same issues on my site. I can't tell what the culprit is exactly but I recently upgraded to Wordpress 3.0.1 and SP 4.3.3. Every now and then, and it is rather random, my pages disappear from the navigation. So at the top bar of the blog I have Home, About and Forum. At times About and Forum disappear from the navigation, therefore people can no longer access the forum. To rectify all I do is edit and re-publish About, that fixes it, for a while.

I went under Options > Styles and turned off the filter, to no avail. Unlike the other user I don't use any caching plug-ins as this is an ecourse site with a limited amount of users. The forum is an integral part of the site hence having the link for it disappear at random times is a nuisance.

Since this particualr site is open only twice a year I can't pinpoint a potential root cause. I know that prior to upgrading to WP 3.0.1 and SP 4.3.3 I never had this problem. I can't replicate it as it is really random but it appears to be only happening at times a new topic is posted or an existing one is removed (not sure about posts).

I also compared my list of plug-ins to the user above. The only common one I see is "Get Recent Comments," none of the others though.

For the time being I'll create a button with a direct link to the forum and add that to the site.

The theme I am using was created by me using Artisteer 2, it's a fairly simple theme without any special features. I've been using it for over a year now and haven't had any issues. It could certainly be that Artisteer 2 is using some older calls for compatibility reasons but I would expect to see the issue show up frequently in that case. Other than the three times yesterday and one time earlier today I haven't had the pages disappearing from navigation again yet and users have been posting new topics in the mean time. It does seem to be very random, maybe some type of delayed update to the database? We do run a second blog on this server with a fairly high usage each day (the two sites are related and are part of our business), that's where a delay could certainly come from. It would be my first inclination. Overall, there haven't been any changes to the site other than WP and SP updates and prior to that everything had been working fine (and I am not excluding WP3 by all means as a culprit). It's really rather curious.