I have a 3.1 site that whilst it was on my testing server I had no problems with it, but on the live server the templates won't refresh.
Things I have tried:

1. Adding ?flush=all to the url
2. Adding ?flush=1 to the url
3. Deleting the footer.ss file, flushing the site (footer still appears), reloading and flushing
4. Deleting the entire templates folder, flushing the site (no effect), reloading and flushing
5. Deleting the silverstripe cache folder contents
6. running dev/build

In case I was having a stupid moment i also uploaded a straight test.html to the server, visited it on the website (it was there), deleted it, visited it again and got redirected to the error page. Which is what I expected.

Anyone know of any other way I might be able to solve this?

I had the same problem due to a different configuration on my (shared) live server.

Everytime you use ?flush, I ended up with a redirect URL of ?flush=&flushtoken=xxx instead of ?flush=&flushtoken=xxx. So the flushtoken never got recognized by the framework and as a consequence ?flush was ignored.

I've added this to my _config.php:

if( Director::isLive() ) {
	// Overwrite arg_seperator.output
	// @see ParameterConfirmationToken->reloadWithToken()
	ini_set('arg_separator.output', '&');
}

Thanks for your reply. Unfortunately that did not work either.

I have now completely deleted the site and freshly installed it with a clean database... and it is still showing the wrong footer.ss.

Hopefully the web host will look into it (although I did tell them about it and told them the easy check to see if the correct one is showing is that there should be a copyright symbol in it and they sent me back a screen shot saying it was there when clearly it is just the word copyright and not a symbol... so I don't have too much hope with them...).

i'm completely stumped.

Where is your template cache stored? I have had issues in the past with permissions on the cache directory that have meant I have been unable to delete cache files with flush=all.

Try manually deleting the folder if you can?

Cheers,

Mo