Ok so I think I'm going nuts. I've got 2 blogs running Wordpress 3. Both use the same theme. Nothing has been drastically modified in either one, but the one is displaying as it should and the other is missing various styles and functionality.
I know the cause of the problem - a 404 error on the one site for two resources. These resources are PHP files stored in the theme's directory in both installations - one is used as a CSS file and the other a Javascript file. But in the one they are both fine, in the other they are exhibiting unusual behaviour.
Basically if you go to the URL for the resource, you will get the content displayed (even though it 404s) but as script-src ref or link-href in the browser the content seems to be ignored (probably as it should be!). What I don't get is why the one blog is returning a 404 for these two files (which definitely exist) and he other one is absolutely fine!???
I can't see any differences in Wordpress either. But this only seems to have happened since the host updated Wordpress across all installations...
To see what I mean: http://www.net-clik.com/ (the broken one) and compare to http://www.chumbo.co.uk/