I have the game I'll try to rip and do some tests today.
Try setting your cache size to 16 sectors (And then 24-sectors if there is no problem), re-ripping the game and not using the ISO9660 mode.
About Jak and Daxter: The Precursor Legacy - Without the FORCE SYNC mode, ISO9660 mode is basically useless at running that game.
That compatibility mode should not be required at all.
If it's required, that means that there is something wrong with the ISO9660 mode that is causing PS2ESDL to either read data very slowly, or to have some other hidden problem