using 29.0.1, version used through official firefox extension page and auto update. No beta. It would seem that this issue is due to the rounded top corners of the active tab in 29.0.1 firefox version. Ran the update to 30.0 which restored full rectangular shapes the issue vanished and the active tabs retained their color and that full size horizontal bar was back below the tab where it should be and not at the top.
so it would seem that the extension doesn't apply the color properly if the tab isn't rectangular