I have a website that, at seemingly random intervals, returns a 404 error for every page on the site excluding the home page. Initially, simply logging into the Dashboard would be enough to fix the problem, now I need to re-save the permalink settings every time.
The bizarre thing is I have a very similar site using a very similar theme and the same plugins, running on the same server without these problems. I've contacted the hosting company and they say it must be one of the plugins messing up the permalinks, but why would it do that on site A and not on site B?
I'm very worried about losing my rankings and about the damage this could be doing to my AdWords campaign.
Did you ever find out an answer for this, I'm having the exact same problem with my own wordpress site.
Kind regards, Leon Coppola