I'm working on a Joomla site and for some reason my site quit knowing it was logged in on the default page. Other pages still know that I'm logged in. Even the default page knows I'm logged in if I include index.php in the url. For example, http://mysite/proj/index.php#home1
works but http://mysite/proj/#home1
does not. I know this was working a few days ago but it has stopped working for some reason and I have no idea why. I've tried restoring to a point a few days ago and that has not worked but since I have no idea why this is happening it is difficult to even know how far back I need to go or weather this is even due to something I've change with the file system.
There is really not much to go on. I can tell you that neither the PHP log or the Joomla logs are reporting anything. I have only one cookie set for the domain and it is for the root and appears to only contain a session ID type hash string.
Update
After restoring a from the nightly backup made last night my site is suddenly working properly again. Unfortunately, as far as I can tell this is the exact same setup I was using this morning which wasn't working. So now the nature of this question has changed slightly. Now I'm just looking for some sort of explanation as to how this could happen so that I can prevent it from happening again in the future.
BTW, while this was broken I had tried loading the page from IE and Chrome on several machines on several networks (internal, external and my home). All produced the same error so I doubt this is a client issue.
Also, when I viewed the source the jmoddiv were all empty so this is probably not a style issue either (IOW, they weren't hidden).
Update 2
I forgot to mention that I'm on Windows (I know, I don't like it either but despite my objections this isn't going to change) using IIS5. So I'm not using mod_rewrite or .htaccess files.