As I posted earlier, I'm having this issue too, with ClassiPress 3.17 and SP 5.0. First I turned off all plugs, to no avail. Then I took out Classipress by switching (preview) to the Twenty-Eleven theme - and voila! SP double menu issue was fixed.
At first I thought it might be with the Custom Search plug-in as it does have the selectBox rules in it. But disabling that plug did NOT help.
So it would seem something in CP is causing the conflict. Sadly there is rarely much help on the CP forums - it takes many days to even get noticed... so this will be a toughie.
Don't know if this is part of it, but I also notice the labels on the left side over-lap a bit with the icons... I've got a child theme working so may be able to address that there.