Before you do anything, Cam, I would get Alan's opinion on this. Clearly this is Logitechs fault...what kind of warranty does the Harmony have? Did it hit 40 quickly before you were able to turn the CD off or was it slowly/prolonged?
I don't know what type of warranty my Harmony remote has, but the rep at Logitech was totally understanding. I called Axiom and spoke to Brent or Brett and explained everything to him, and one thing that he did mention was whether or not the volume got to 40 really quick, and I just mentioned to him that it was gradual but it was probably around five seconds (my RPA-1 didn't even shut down, so it was fairly quick). I'll fire off a message to Alan regarding this.
wheelz999,
When I got my URC's MX900 and MRF350 (the RF base), it had an RF sniffer mode. I had to run around all over the living room to find a decent spot that didn't have has much RF interference. In the end, it ended up on top of my closet covered with a Frisbee! That's what it took to quite down the RF. It's very possible that you're getting so much interference that it cranked up your volume. I'm not sure if interference can do that or not, but it's something to check out.
The Logitech rep said that it couldn't be any interference and actually suggested to try updating the firmware.
Also, just in case it happens again, I set the "volume limit" on my Denon to 0.