For my notes, check the versions of the following -
Bios
Command Center

Alienware Bios : A02

Command Center: The Newest version on the dell website (2.5.35 A02 I believe)

Thank you Chris for your concern. I was on the telephone support line yesterday and they used Aliencontact to connect to my computer to try and resolve the issue. She completely removed the command center software, reinstalled the newest version, and the problem still exist. When the computer shuts down and starts up, command center doesnt work (ie. fans are on high and the active venting lights and side lights dont work) until the computer is rebooted. The result is believed to be a faulty alienfx board and I'm in the process of replacing the board. I'll update you further if this resolves the issue. Thanks again for your concern.

kiax0001

Here are detailed procedure to diagnose and recover the MIO and ACC (Alien Command Center) 
1. Open the Control Panel, by left click on the Start Button
2. In the Control Panel, go to Programs and Uninstall Alien Command Center
3. Open Windows Explorer, by left click on the Start Button and by right-clicking on My Computer in the Start Window
4. In Windows Explorer, click Folder and Search Options
5. In Folder Options, choose the View tab and enable “Show hidden files and folders” and click OK
6. In Windows Explorer, go to C:/Program Data/Alienware/Command Center/Thermal Controls and delete the Profile.xml file
7. In Windows Explorer, go to C:/Users/Your name/AppData/Local/Alienware/Alienware AlienFX/Themes and delete all *.ath files
8. In the Control Panel, go to System and Maintenance/Device Manager
9. In Device Manager, open Universal Serial Bus controllers and ensure there is no Unknown Device
10. In Windows Explorer, open C:/Dell/Drivers/ACC release number and double click on the Setup.exe file
11. Complete the Alien Command Center installation by answer “Yes” to all dialogue pop-ups
a. During the installation process, a MIO FW update will occur
b. Do not force or allow any shutdown at this time!
c. If repeating this MIO FW update due to prior installation failures, please capture a screenshot of the FW update dialogue window
12. Allow the system to restart
13. In Device Manager, open Universal Serial Bus controllers and ensure there is no Unknown Device
14. Launch the Alien Command Center icon on the desktop

If steps 9 or 13 result in an Unknown Device, or no device is detected, attempt the following steps:
Ensure the MIO USB cable is properly connected at both the MB and the MIO
Shutdown the system and pull the AC plug.  Repower and restart the system after 30 seconds without AC power

Hi Kiax,

I'm wondering if you had the Alienfx board replaced and if the replacement solved your problem with the command center?  I am having the exact same problem as you are.  I'm not sure if I understand how this could be a faulty board though, since the command center works on restart.  I don't know anything about the workings of computers, but this is my line of thought:  The problem lies somewhere in the difference between a regular cold start and the restart.  I don't know what that difference would be.  Maybe Chris, or another knowledgeable support person would know.

By the way, I also have all the updated drivers, etc.  I also tried the uninstall & reinstall as described by Chris.  I opened the case to check the connections Chris mentioned but the MIO is difficult to see and reach as it's obscured by bundles of wires.  From what I could see, everything looked okay.

Hey Easiest,

I'm glad to know that I'm not the only one experiencing this issue. I'm having an on-site technician come and install the new MIO board soon so I'll keep you updated on what happens. Personally I think it has something to do with boot during BIOS and the board itself. I've noticed that while its loading the BIOS (after the restart) is when  the lights turn on and the fans begin to slow down.

My current work around to this problem is when you cold start the computer, press F2 to go into the bios and just select the "Save and restart". This will automatically restart the computer and the lights start working again. This is a whole lot better than having to wait for your computer to load windows and then restart.

Chris or any technical liason, please take a look into this problem and keep us updated.

Thanks.

P.S. On a side note, does anyone have a aurora or area-51 with two 5870's in crossfire? If so, can you please verify if both of them are showing up in GPU-Z as PCI-E 16x bandwidth? For some reason 1 card running at PCI-E 16x while the other is at PCI-E 8x. I would be really disappointed to find out that these motherboards don't support 2 PCI-E 16x slots.

Kiax

I just got an Alienware Aurora pc, and i'm having a similar problem, except i can't get it to work even after a reboot.  I am showing an "Unknown Device" in the device manager under USB devices, which Windows cannot automatically update.  I've searched the Dell site but haven't found any relevant drivers, and reinstalling the command center doesn't fix the issue.  Is there somewhere to download this driver?

Hi pbseaton,

This happened to me too the other day on a restart.  All I had done prior to the restart is unplug an external hard drive from the USB port on the top front of the case.  I shut down the computer, unplugged it, and checked inside to see if I could see anything disconnected but I couldn't.  I plugged the computer back in and strangely enough it was fine again.  In fact, I discovered if I unplug the PC when I'm done for the night, and then plug it back in the next day the command center works, i.e. it has a similar effect as the restart.

Hey Guys,

So a quick update. The on-site tech came out to install the new MIO board but it was the wrong part. He went back to order the correct part and for some reason it won't ship because this part requires management approval (go figure). The on-site tech was nice enough to process an exchange so I'll be receiving a new computer with the same specs in the next 10-15 business days. From what it sounds like this is a common problem and I'm afraid my new system may inherit the same issue. I'm hoping it's software related and not hardware.

 Chris or any other technical liasion please get back to us and let us know if dell is in the process of fixing this issue. I would appreciate feedback on this.

P.S. The on-site tech said that these motherboards should have 3 PCI-E 16x slots so if your not getting a 16x bandwidth for any of your cards make sure your ordering a new motherboard. I guess my new system will hopefully knock down two birds with one stone if it fixes both of my issues :) I'll keep you guys updated.

Thanks,

Kiax