I have a 2006 Hybrid as well. I have had the exact same problem with my windows only in my car it was front passenger. Fortunately, the Honda dealership here is pretty straight. After the second time they ordered a new motor- make those guys do it for you too while it is still under factory warranty!
Recalls I expected... none too big of a deal that they couldn't just be scheduled with the oil change.

I have a rack on my car for surfboards, kayaks, etc. and if obviously effected the fuel efficiency a little bit. All in all though I am REALLY happy with the car. The features on the stearing wheel, auxilary i pod plug in... it all rocks. I can't wait til you can lower the back seat again though like in the normal civics!