Turn off summer board compatibility, the slider just above the browse themes button. Winterboard was one of the first things I installed and while not every UI mod works, many things do. Themes and mods to signal bars and font colors work, but mods to lockscreen sliders don't for example.
Have fun!
I've been running Winterboard with SummerBoard Mode set to On, Solid Status Bar, No Docked Icon Lables, and Random for iPad all selected. I have not had one problem or even noticed any random craziness. Works just like my non jailbroken iPad just sexier. I was under the impression that Winterboard was all good.