was told of 404, saw it, logged in and its fixed, why?

You received this 404 on your home page when you accessed it through your URL? And when you logged back out, you could still access not through your panel? We don’t really know what happened from the one incident, if it continues to occur and you can reproduce it at will then we’ve got something we can look at. Until then, it might be a little early to do very much worrying.

it is never on the homepage. Its always on the pages after. Even if i go to a sub page directly, it will happen. The page stays live for around 4 hours before it returns to a 404 state. I have in the past just reset permalinks and it back for 4 hours or so, but today i just logged in and checked and it was back up. When logged out after logging in the page is live for the 4 hours or so. Could it be some sort of hosting cache? my .htaccess is a large file from the W3 cache pluggin, could this be it? I use Cloudflare from the hosting, Could this be a problem?

Could be caching, try clearing your page cache.