first of all v5 is not a new system the current ps2 revision is version 7/8
if the only function that is not working correctly is dvd original and dvd movies + backup dvd-r the problem is with the cd/dvd controller the first check to make is point S is secured correctly or is not shorting against any other point's, i presume all other feature's are working ?.
So this rules out the problem being the bios wire's, if worst comes to worst and the above point is not the problem i advise you to resolder just the cd/dvd controller wire's taking great care on how you route the wire's and making sure every point is in the correct place from dms3 to mboard.
On a last note when a dvd format disc is inserted do you here any adverse sound eg, clicking or constant seeking/reading noises including clicks ?
"Light travels faster than sound. This is why some people appear bright until you hear them speak"