Well, in the Once in a Livetime CD book, he's playing his old Ibanez and on Live Scenes in New York, he's playing what appears to be an early sparkle version with no arm cutout. So, I would estimate either Metropolis Pt. II or Six Degrees of Inner Turbulence, depending on if he got the guitar for the 2000 tour or before.
Six Degrees was the first time he had what we know of as the production version of the JP6. IIRC, he used Ibanez to record SFAM, and the EBMM protos came out on tour. Basically what Ernie said.