1) I believe you. My 1st gen Air had heat issues.
2) My 27" I believe does not have this problem.
Bought last monday, (26th Oct) and has been on moister of the time. It was 35 degrees today in South Australia, that's 95 F. Pretty much all day the iMac has been in WinXP in bootcamp, playing Colin McRae DiRT in 1920x1080 (it's a 27" model, but 2560x1440 produces a low frame rate in this game) and i've been playing this game for a good 7 hours solid today. The back of the iMac has got VERY hot. I've also done much number crunching/ batch converting video files in OS X. Playing a 1080P video file full screen in Quicktime Player X uses 75% cpu (remember as it's dual core, percentages can go over 100)
3) In your activity monitor shot, you show Adobe Flash player using 108% cpu. When you movie file is open, playing jumpily, out of interest is Safari closed (not the window, is the blue dot under it?) The Mac version of flash player is total pus, and i've often seen it hog ~200% cpu or try to.
4) Pop iStat Pro in dashboard, and grab SMC Fan Control too. You can see the temps for all 8 temp sensors in iStat Pro, and the fan speeds for the three fans, and with SMC fan control you can jump the minimum fan speed manually. You shouldn't have to do this, and don't want to have to do this, but this might help narrow the problem/provide a work around for you. My iMac the hottest thing is the north bridge, getting to 65 degrees at times. The fans are designed to spin up to higher RPM's if needed, and at this level, they don't, they're mostly sitting around 1000 rpm. If i manually ramp the base fan speed for all fans to 1500 rpm using SMC fan control, the iMac runs very noticeably cooler to the touch, and is still quite quiet. For fun, i created a profile maxing out the fan speeds. WOW this thing is loud set like that

But my point is, you could try ramping it up to the mac fan speed to see if your slow down is heat related or not.
5) Play your movie file after a restart, check activity monitor, how much CPU does it use to play it? When the slow down is occurring, how much CPU is it using then to play your movie?? If there anything else showing high CPU usage at this time?
I'm really most interested to know, and good luck.