I just found out that the "new" PSU is ironically a very old ATX 1.1 model, while my stock is a ATX 2.2. Old ATX models would use the pin 20 (-5V), but is no longer required for newer ATX models. I am still unsure if that is related to the disk boot failure.
Also, my stock PSU has 1 more amp on the +12V rail than the "new" PSU.. go figure.
I'm just going to buy this PSU and discard the "new" PSU. Great, there goes $40. >.>
http://www.newegg.com/Product/Product.aspx?Item=N82E16817171031
Two 12V rails for a total of 36A and ATX 2.3 to go at that. Should be plenty.