I think this problem has been caused by Better-WP-Security (ironically).
I installed the plugin earlier this week but didn't look at my site (Fossenet.co.uk) again until this morning, when I found I could not login to the admin area as clicking on the admin link just resolved to the homepage, as did typing ...wp-admin or wp-login in the address bar.
Following some other advice I renamed a couple of recent plugins (this one, and Pricing Table Pro) along with the Catalyst Dynamic theme folder.
That enabled me to login, so I re-enabled and renamed plugins one by one. When I renamed and reactivated Better-WP-Security I was immediately logged out of the site and now everything apart from the homepage is a 404 error. The site is totally broken.
I have tried changing names back again and even moving the plugin out of the directory altogether but that hasn't altered it.
I also replaced the .htaccess file with a blank one, and subsequently one with the recommended rewrite code from the permalinks codex page.
Site is still broken and I haven't a clue what to do. The irony of course is that in attempting to protect my site I appear to have broken it...
Any ideas anyone?