It is the editor's opinion that the Creation Matrix and the Autobot Matrix of Leadership are two separate things with completely different properties.
Sometime prior to his arriving on Earth, Optimus Prime was given the Creation Matix. When Shockwave appeared on Earth, he and the Decepticon took over the Ark, deactivating all the Autobots except Ratchet (who was not there at the time) and Optimus Prime (whose head was needed active so they could use the Creation Matrix). In this way, Shockwave planned to use Prime to create the Constructicons. After programming 6 microprocessors, Buster Witwicky arrived at the Ark with Ratchet. Buster went in to say goodbye to the Autobots forever, but instead saw what had happened. Optimus told Buster to take the wires connected to the Autobot leader's head and press them against his own The result was an immense electrical shock. Buster came to a short while after and Ratchet drove him home. Buster realized that he now possessed the ability to both mentally manipulate metal and to understand even complex electromechanical devices. What neither he nor the Decepticons knew was that Optimus Prime had transfered the Creation Matrix program into Buster. Shockwave took Optimus's head to G.B. Blackrock's Aerospace plant#1 in Portland Origon, to build the bodies for the Constructicons. When Shockwave found out that Prime didn't have the Creation Matrix program he tried to destroy him, but the Autobots saved him and he got the Creation Matrix program back from Buster.
Optimus next used the Creation Matrix to give life to the Aerialbots, but when they almost killed a human, he had wiped out thier programs and reinstilled life into them via the Matrix. Unknown to Optimus, Bombshell had planted a cerebro-shell in him, allowing Megatron to tap into the Creation Matrix, giving life to the Stunticons while Optimus was recreating the Aerialbots.
Following the battle in the video game "Multi-World" with Megatron, Optimus Prime's dead body was shot out into space, with the Creation Matrix inside of him (At this point, unknown to the Autobots, the Creation Matrix was a physical object). Years passed and the Creation Matrix crashed moon called VsQs in a far off solar system. There, it was exposed to hatred, death and chaos.
When the Pretenders Grimlock, Bumblebee, Jazz, Bludgeon, Stranglehold, and Octopunch battled in the center of Cybertron, they awoke Primus, thus alerting Unicron to Primus's location. The Autobots went searching for the Creation Matrix, splitting up into four teams. One team (Hosehead, Siren and Nightbeat) went to the planet PzZazz and came up blank; to make things worse, they got the attention of the Decepticon Thunderwing, who captured them. The Second team (Backstreet, Override, and Dogfight) went to the planet Cheyne and came up with nothing as well. At this point, Thunderwing learned of the Autobots' quest and sought to get the Matrix for himself. Thunderwing battled the third Autobot team on the planet Gottlieb, and ended up learning of the Matrix's true location on VsQs. Upon arriving there, he met Grimlock, Jazz, Bumblebee and a creature mutated by the Creation Matrix. Thunderwing got the Matrix and went to the Ark, managing to enter unopposed by using Grimlock's shuttle. The Autobots battled Thunderwing, but he was too powerful, being able to tap directly into the power of the Matrix. In the meanwhile, Nightbeat, Hosehead and Siren had hidden aboard Thunderwing's ship and Nightbeat managed to enter Grimlock's shuttle unseen. Surprising Thunderwing, he was able to harpoon the mad Decepticon and attach him to Grimlock's shuttle, which was ejected into space and detonated.
When Unicron attacked Cybertron, Thunderwing (repaired and revived by the Matrix) appeared and fought Unicron. Optimus Prime obtained the Matrix from him, went inside Unicron, and opened Matrix. This destroyed both the dark god and Optimus Prime.
Looking for a way to repair the damage to the planet Cybertron (a result of the Unicron War), Hi-Q and the Neoknights searched Cybertron for the Last Autobot. Upon being located, the Last Autobot recreated Optimus Prime (combining him with Hi-Q permanently). Somehow, the Creation Matrix was also recreated inside of his new body.
Years later, a new threat appeared in the form of the so-called Cybertronians. In a battle with Megatron, the Creation Matrix was ripped out of Optimus Prime's chest cavity and placed aboard the Decepticon Warworld. Starscream, working with the Cybertronians, stole it and used it to merge himself with Warworld. Battling Megatron and Optimus Prime, Starscream came to realize that the Creation Matrix was in fact recreating him into a force of good, and he returned it to Optimus Prime. The Swarm came to Earth and Optimus Prime was devoured by it; as it touched the Creation Matrix, the Swarm was converted to the cause of good and repaired Optimus Prime. It is unknown if the Creation Matrix was also recreated in its entirety.
Rodiumus Prime also encountered an evil presence within the Matrix. He battled with the presence until he regained control.