you're 100% positive that the ports are USB 2.0?
first step: double check that.
second step: check the cable you're using to connect the drive to your computer. is that USB 2.0 as well? if it's an older drive or if you found a cable in the basement or something it's possible it does not support usb 2.0 transfer speeds.
if they are both USB 2.0, download nero cd-dvd speed and, with a disc in the drive, run a "burst rate" test and let us know the results...it's possible that windows is just acting strange and your transfer speeds will be fine.