I have heard about the problem with PTP , but this machine cannot even boot the disc at the beginning.
Any other discs had no problem , dvd film , original PS2 games on CD and DVD single layer , and also backups with DVD-R.
The version of the machine is as follows SCPH-30003R it came with the metal gear solid 2 game.
According to the following site this makes it version 5 or 6.
http://www.playstationchips.co.uk/pages/versions.html
I dont think it could be the messiah chip because it boots everything else , it must find it harder to read the boot section of the DVD dual layer game , as i mentioned before i read on this forum that would likely be a reason why older machines cant do it , because the boot section is harder to read compared to a single layer game. Strange because i thought it would boot and the problem would be like you mention , difficulty in reading second layer.
Maybe the best thing to do is make a backup on dual layer DVD-R and patch it , or failing that a new laser?
I suppose a new laser might be expensive compared to just buying a new machine these days , although id rather not have to bother.