From Tom:
So far as I can tell, it's something to do with the SEO friendly links. For instance, on EnergyBlue, there's a whole load of excludes specified but panels are being displayed on these pages regardless.

Hmmm, it cant be anything to do with the SEO friendly urls, because they use mod rewrite so in reality the url may be http://eocms.com/forum/panel-excludes-not-working.893.html for example, but the system will still see it as....
On second thoughts, this may be the problem, I will do some tests on this site in a bit, print out the query string and see what it outputs on those pages that are meant to exclude panels...

Nothing to do with the SEO Friendly links. Its to do with the fact that we excluded panels from the homepage by using ?, so it only excludes those panels on the homepage, it is ignoring the rest

TGPEG can you confirm this is fixed please?

Yes indeedy it is fixed.
This bug has been deemed [Fixed] by an eoCMS developer. If you dispute the Fix, please PM a developer, giving details of why. This topic can then be unlocked allowing for further discussion.