Somehow you had not gotten the new code event listeners for Beta 5, so XenForo couldn't handle a dynamic wiki route. Running the upgrade script again fixed this problem, but revealed another issue, which showed the same error message in the OP.
There was no XenForo handling for non-friendly wiki URLs. Only friendly wiki URLs would pass to a page, otherwise the route would fail. Fixed in your test install and in build 005.
The data for the wiki index page gets cached. To clear the bad route for the wiki index, go to the VaultWiki Admin Panel, Settings > Site Config, and change the File Name to just "wiki". This should clear the cache entry for the index, as well as make your URLs slightly prettier. Just my opinion, but I think this name looks better for XenForo's URL structure (and I believe it's the default now for new XenForo installs).