Couple things for you. First, I'm not too familiar with your w407. I do have a w505 so I'd imagine they are similar.
I never had my unit wired up the way its supposed to be factory. IE, I bought mine with the TR-7 bypass, so I don't have to fool around with ebrakes, brake pedals or any of that stuff. I'm assuming, since you didn't mention that (only PAC, Ipod integration or something?? I've never used it so I'm not even sure what it is //content.invisioncic.com/y282845/emoticons/smile.gif.1ebc41e1811405b213edfc4622c41e27.gif)that you don't have that bypass... Might be something you would want to look into for your model.
From my understanding, to use the video portion of your head unit (has video doesn't it?), the ebrake has to be engaged. That in turn grounds something in the harness and allows for additional features (video, etc) to be viewed... can't be driving and watching movies, right? Why that would be the case for your clock and whatnot, I have no idea. In fact, it might have nothing to do with it at all //content.invisioncic.com/y282845/emoticons/smile.gif.1ebc41e1811405b213edfc4622c41e27.gif
Assuming this has DVD video capabilities, does video work on it? I was having trouble with video, and overall features when I installed my head unit also. I bought it used and thought it was broken, so I wasn't too happy. After feverishly going through the manual I found that there were two switches on the unit itself that needed to be in the opposite position. I flipped the switches and everything works as it should.
So while I don't know if you're having the same problems I did, you can atleast give these a try. Also the bypass is a good investment for future reference.
Michael