The original Command Center software corrupts the C2 chip that controls the lights sometimes.. it has to be flashed. You can google it and find this :http://en.community.dell.com/owners-club/alienware/f/3746/p/19442434/20203326.aspx#20203326
LDSISHERE finsihed the solution for us.. my shop is offering to do this for customers if they are non-techie/do not want to invest in a programmer for the chips.
Your issue may not be the same.. but if the software reinstalls do not help etc.. then it may be time to turn to the reflashing option. I'm located in MA.. LDS is also offering to fix these since he built a programmer.. you have to ship it to him. We are located in Bridgewater MA. [Central Square Computer Repair]
See the thread for details as they are quite involved.