I wouldn't use Thompsons on Sunbrella as they do not recommend it, but perhaps it works on straight cotton canvas? It's just a silicone-based product. Nothing too harsh.
I'm going to be a +4 on 303 products. My 9 year old Sunbrella is still going strong as are my 9 year old clear panels ("Isinglass"). I 303-treat the Sunbrella only when it starts to leak. I 303 the vinyl every 30 days. NOTE: My enclosure is up 365 days per year in MD (1 month of that in FL/Bahamas).
Rusty - same here in Rock Creek/Pasadena. It's got the be the planes and the coal power plant. I've been other places with all kinds of rain and no black streaks at all. Sometimes, even in Pasadena, if the wind is from a different direction, no black streaks either.
To the OP - before you treated your canvas I think it's possible the dirt was working itself into the fabric. After you treated it the dirt ran off and made the streaks on your hull.