I believe that second license is more correctly the third amendment to the original license with some additional support from Iterated added. It was also in those posted filings online didn't you guys bother reading any of them? They seem to be gone now but you can always ask Panik for a copy he probably has one.
The explanation may be that Dimension didn't bring up this "third amendment to the original license" in court. They sought and obtained a declaration that they owned a license to PVS/SGI code. Perhaps Fracked was inventing the 2003 license, and/or perhaps he was bringing it up to explain away the curious fact that Dimension seems to be in possession of code that is different from that which DFMI is licensed to use.