Uploading in binary mode changes a number of things, including but not limited to the line-ending method used in encoding the file and possibly the MIME-type used to announce the file to the browser.
Normally "automatic" is sufficient, provided you haven't told it to "automatically handle" certain files as binary which are normally handled as text (ie: CSS, PHP, HTML, JS etc)
I am going back to check if any files were uploaded recently as binary mode.
No, it's actually supposed to be 2 slashes with "css" between them: /css/
I suspect you've done some hard-coding in the html_header.php file in your custom template to force loading of a stylesheet from a non-standard location.
To state my point more specifically ... you don't have your main stylesheet in the normal location, and your template is calling it from that non-normal location, which suggests you have also uploaded custom template changes which alter the normal stylesheet loading procedures. It's difficult to know which if any of these factors plays a part in the problems you're experiencing.
I'd be inclined to re-upload your stylesheet files using ASCII mode specifically (to current locations, not worrying about folders just yet) and see if that helps. Then deal with folder locations later.
In that case, I think the 2 slashes have been there for a while and it was not creating problems. For some reasons, the template suppliers made 2 stylesheet.css file one is inside /includes/templates/CUSTOM while the other is inside /includes/templates/CUSTOM/css. I don't think this is an issue as it was working fine just a week ago. However, I might have to try re-uploading the files later.
I suppose that depends on which mod you're using. What do its instructions say about turning it off? Or about de-installing?
Naturally, de-installing is a more sure-fire way of knowing that it's not affecting things incorrectly.
Remember that there are likely .htaccess settings that affect the mod as well, and may require editing if you disable or remove the mod.
I am using Ultimate SEO URLs v2.100. Seeing that nobody really know how to turn in off outside of the admin, I will try uninstalling it by reversing what I have done.
If this all happened "suddenly", were there some sort of coding changes made just before this happened?
Not sure, if I had, it's probably some minor changes to make the website look better.
Were there any server changes? Are you seeing any errors in your server's "errorlog" ?
My hosting company claimed that there weren't any server changes. How do I find out if there is any erros in my server's errorlog? My hosting company is also helping me to solve these problems. So far they have reload a backup from a week before and moved to another server. However, the problems persist.