Hi,
I really don't know whats causing this for you but one possibility is a low memory environment. I've seen strange things happen when memory is very constrained. Probably some error occurs due to low memory and the sitemap ends up not getting fully populated and it goes into the cache not populated so it appears pages are missing. In this case recycling the app pool will resolve it but it may recur. Some hosting environments are very constrained, especially at low budget hosting providers.
I would recommend first thing to upgrade to the newest version of mojoPortal. If the problem persists or recurs I would kep an eye on whats happening in the error log. There may be other errors leading up to the timeout error that would give a clue to the nature of the problem.
Best,
Joe