i dont think it has ever been documented what triggers the "system files are corrupt" message.
if i had to guess, i would say it has something to do with writing that playlog bullshit before booting the game.
if i were trying to track down the cause and fix it, i would first use
nandBinCheck . there are lots of things that it is able to detect that there are no other tools capable of detecting. run it first on your working nand.bin. and then on a bbricked nand.bin and see if there are any differences.
if this doesnt turn up anything, i would open each nand.bin up in
nandExtract compare file permissions and stuff like that.
if you still havent come up with anything that jumps out at you as the cause of the brick, i would extract both nand dumps with that tool and compare them on the file level.