You have several options how to include resources (e.g. css files) that include query parameters. What does not seem to work is to add such a style sheet reference via the Resources \ Style sheet option.
However if you add the reference as a linked resource things seem to work e.g.
rel=”stylesheet” media=”all” target=”_self” charset=”UTF-8″>
I am not sure if this is the proper or preferred way to add such resource?