With my PS2 and modchip, the PS1 original ejects automatically (for 4 secs) during which time we insert the backup game. Does your PS2 behave like this? If not, I'd suggest that you're into a timing game for pushing the eject button. I chose my modchip carefully so that there would be a formal occasion on which to swao the CD rather than judging when to push the eject button.

Also try one copy without patching for PAL. If it works (greyscale) then suspect the patching unless one of the failed backups works on the odd occasion as you indicated; in which case Timing is my hunch.