theme still use caching even when flushed cache and using devel
Since it sounds like you've got all the Drupal-related items checked, perhaps it's worth a shot in the dark...

Pull up the site in Chrome and inspect the element that's supposed to have the updated colors (right click and select "Inspect element"). This may reveal one of two things:


Click the "Computed" tab in the right-hand column. Is your color change being overwritten by a more specific declaration? (eg: #foo .some-class { ... } will supersede .foo-class .some-class { ... } regardless of the order in which they appear)
Perhaps you've been editing the wrong file? I know I've done it before...  Click the Sources tab and make sure the page is loading the file you expect it to load. Make some random changes, reload and check that those changes show up.


Hope that helps.