I use a similar arrangement: two 20" monitors side-by-side at a total of 3200 x 1200. Of course I have the dock at the top: I think it's rather a shame that Apple haven't fixed this properly yet - I gather that options to have the dock at the top, or towards the corners of the screen, were available in the System Preferences of the original OS X beta, but they were removed for OS X's release.
You can see my configuration at
http://mac.stroller.uk.eu.orgChapter 3 of "Mac OS X Hints" is available for free download from O'Reilly's website, and explains how to achieve this setup.
Back to the original question: I don't seem to have clock.app included in this build of Panthar (7b49), so I can't look at your example! But I can confirm that top-dock handling is somewhat improved in Panthar. I see now that this doesn't in fact answer your question, because you're talking about the MENU bar, not the dock. I absolutely detest Apple's handling of the menu bar - I think each window should have it's own, like in every other o/s. So sorry I can't help you, but I hope someone has enjoyed my ramblings.
Stroller.
