What is the difference between erasing HDD in PIO (slow) mode or in ATA mode (when HDD is autodetected by BIOS)?

I am asking this becouse I have tried both ways and got better results after erasing in PIO mode. After I have erased HDD in ATA mode and scanned it, it had some green boxes, and after hiding it in BIOS and repeating the same procedure (very slow, almost 12hrs for 60GB hdd), the green boxes dissapeared (only gray boxes left).

So is it because PIO mode is slower and "more thorough" or just after second erasing HDD became better?