Upgrade to 1.6 made navigation menus disappear

I upgraded to 1.6 and my navigation menu and other custom menus disappeared from the post script bottom region in the Acquia Marina theme, and from the left column in my admin theme, Root Candy. Everything said they should be there but they weren't. Rolled back to version 1.2 and the menus reappeared. Only the masquerade module block didn't disappear.

Also, after the upgrade the javascript version was default and since the CSS is completely different it looked completely wrong and (I think there's already a bug report for this) the box would not open.