Hey fellow Oregonian...
I've been playing with mine... so far haven't really noticed. I rode to work all but one day this last week (had to haul something to work a litle big for the bike, but could have done it, just would have been funny looking)
Anyways, you know what our weather has been like this week... One of the first nastier days, I rode with one side open, and the other closed, and couldn't really tell much difference, but like you I had good gear on, and I had the insulating liner in...
That said, I did sort of feel like my side with the vent closed (in) felt a little cooler, but it could also be sort of a placebo effect. It would make sense that it should help, just looking at the angles, it seems like when open (out) it would direct air away more... I also rode one day in either normal pants or without a liner, and I could have sworn my hips felt cooler with them open than closed... but it might be it was just directing the air out that way further and hips instead of legs...
I'm still playing with it, I've got a small screwdriver I'm carrying in my coat pocket so I can change it at any time...I'm going to work this morning, and it will probably be decent when I ride home (2pm) so maybe I'll do one in, one out again and see if either feels cooler or more wind on it (if I can ride without my overpants, asuming it's warm enough).
I think a ride in mesh pants or (gasp) shorts (wouldn't catch me doing it in shorts) would be the best way to know, you'll have the most feeling on your legs. To me it seems pretty well sheltered anyways, but my last bike theoretically should have been more sheltered, it tended to direct a LOT of air on my legs, and in either position the FJR is FAR warmer in the cool weather than my Piaggio MP3 ever was (even with it's windscreen which is actually taller than the FJR.