Ok I just got it fixed since I remembered the problem happened when I had ehci usb enabled which the only way I think they affected each other is that they are on the same irq. So in the end I can use the old behavior as long as I have my ehci usb ports disabled. luckily my only usb devices are keyboard and mouse and I also have ohci ports.
Like I said I think the problem was explained with this dmesg output where at the end it says irq #11 was disabled. (my SATA stuff is also on irq #11)
irq 11: nobody cared!
Disabling IRQ #11