Eisenglass (clear PVC) can be polished, as Mike suggested. In addition to the products he recommends Meguiar's PlastX (get it at a chain auto parts store) is a good one for polishing clear plastics. I have also used Finesse It II form 3M. Also, the Yacht Brite folks recommend their Buff Magic product, which other RO's here have conformed works well on clear PVC.
If it looks like rust but there is no matching rusty part, then it is probably as Mike described - scorching. Is there a stainless support in that area? If so either use a window protector or a cover over the stainless where it can contact the window.