Joomla, SEO and the case of the disappearing CSS

I’m helping maintain a new website with a basic Joomla install.

Things were working fine (apart from a horrible theme someone had selected), until I started playing around with SEO options (in the global configuration):

SEO Options - don't touch!

The little exclamation mark pops up with:

WARNING!
Apache users only! Rename htaccess.txt to .htaccess before activating.

I figured, “hey, I’d like this site to be googlible, why not enable the first option?” Big mistake – something in Joomla says, “Great, your links are now cleaner, but now watch all your CSS and images disappear!”

And so any link off the first page comes without CSS or javascript or images…!

(Of course, it took some digging to realise those options were the problem..)

So a solution?

Well, there’s talk of modifying some of the php config files in the above links, but since this isn’t really my website to be hacking that sort of stuff, I’d prefer a longer-term solution that would be upgrade-proof (other than not to use those options at all)

Here’s one solution that could work, and doesn’t seem too ‘hacky’ from teachmejoomla. I’m waiting on FTP access to the server, so if I have that as a backup option in case of emergency, I’ll give it a go.