Just a note from from another new Colorado (Fort Collins) 390BH Berkshire owner. We picked ours up last September and had a few of the same problems you had on our inaugral trip:
1) Mud Flap - I actually caught ours fairly early and didn't completley ruin it - had to trim the bottom rubber off to make it look ok. I was told by Forest River that, if not covered by warranty, it would be over $900 to replace.
2)Night/Sun shade problem - we didn't have the problem while driving, but did thereafter. Re-programmed it and didn't have a problem again.
3) Drove throught 50+ mph winds and had the exact problem you had. We actually pulled over and waited the wind out - extended the slide and retracted it. The awning rolled up fine. We haven't had the problem again. Would like to hear if you come up with a fix for it. Its was completely nerve-wrenching having the problem. Like you, I thought the awning was completely going to rip off!
Anyway, hang in there - we absolutely love our rig. It's been in storage since last November, but we're about to break it out for the season and we look forward to many trips!