We found a solution that may help. Our menu was displaying, but expanded the entire thing out as an unordered list. We're on DNN 5.6.0 and using the DNNMenuNavigationProvider.
We installed the DDRMenuNavigationProvider here:
http://dnnddrmenu.codeplex.com/
With detailed instructions here:
http://www.dotnetnuke.com/Resources/Wiki/Page/DDRMenu-user-guide.aspx
We simply then went into the skins and updated the same dnn:NAV controls to use the ProviderName="DDRMenuNavigationProvider" and the menu came back the way it was, with an extra sliding flyout animation.
Hope that helps.
Update
In addition to updating the navigation provider, and the user agent as described above, we also updated the \js\ClientAPICaps.config file based on these instructions:
http://support.dotnetnuke.com/issue/ViewIssue.aspx?ID=13964&PROJID=2
We reverted the update for the dnn:NAV controls back to DNNMenuNavigationProvider and everything went back to the way it was operating before.