Hi Andy,
Light cloudiness in awning windows is often a sign that you were rushed when you folded the awning the last time you used it. You need to take care folding around the window areas.
These light cloudy marks should come out if you properly tension the awning, especially on a hot day - or borrow a hair dryer and be very careful - you don't want to heat the plastic more than blood heat.
If you have deep marks in the windows, then you are probably stuck with them - it's a characteristic of the plastic if it gets too tightly folded.
Robert