The official NTSB accident report reads, "The National Transportation Safety Board determined that the probable cause of this accident was fuel exhaustion and total loss of power from both engines due to crew inattention to fuel supply. Contributing to the fuel exhaustion were inadequate flight planning and an engine malfunction of undetermined nature in the right engine which resulted in higher-than-normal fuel consumption."
It was known that the right engine's magneto — a small power generator that provides spark and timing for the engine — had been malfunctioning (Powell, among others, spoke of seeing flames shooting out of the right engine on a trip just prior to the accident), and that pilots McCreary and Gray had intended to repair the damaged part when the travelling party arrived in Baton Rouge. It is possible that the damaged magneto fooled the pilots into creating an exceptionally rich fuel mixture, causing the Convair to run out of fuel.
It was suggested on the VH-1 Behind The Music profile on Skynyrd that this was the case, or that the pilots, panicking when the right engine failed, accidentally dumped the remaining fuel. Pyle maintains in the Howard Stern interview that the fuel gauge in the older model plane malfunctioned and the pilots had failed to manually check the tanks before taking off.
http://en.wikipedia.org/wiki/Lynyrd_Skynyrd