I’m afraid I haven’t been able to find the problem so far.
I wanted to install Ubermenu on my own test setup to analyze it more, but since they don’t have a free version available that’s not gonna work.
From what I can see, the way Ubermenu works, it is basically incompatible with the way my plugin works (or vice versa). The only thing I can think of it to add a workaround in your jQuery code that would make the clone act like a regular Ubermenu. Something like this:
$('#navigation').on('click', '.cloned a.ubermenu-target', function(e){
if ($(this).parent().hasClass('ubermenu-active')) {
$(this).parent().removeClass('ubermenu-active');
} else {
$(this).parent().addClass('ubermenu-active');
}
});
This is just a guess (I can’t actually test it myself) and may not work, and even if it does, it may not work perfectly so perhaps some additional coding is required.
Unfortunately, that’s all I can come up with at the moment, but I would suggest getting in touch with the Ubermenu people. Perhaps they can help a little further.