I would assume its to do with the Tuner & chipset. There are different tuners/chipsets out there and many do better than others (most USB have smaller newer tuners)
Its not the PCI, since (1) PCI has more bandwidth than USB2, and more crucially (2) USB ports are routed though PCI.
Many PCI boards still have older chipsets from when they were first "launched" (there are newer PCI cards with newer chipsets on, but these tend not to be the basic models) where as the USB2 dongles are new configurations and so tend to have newer chipsets.
Its not the PCI, since (1) PCI has more bandwidth than USB2, and more crucially (2) USB ports are routed though PCI.
Many PCI boards still have older chipsets from when they were first "launched" (there are newer PCI cards with newer chipsets on, but these tend not to be the basic models) where as the USB2 dongles are new configurations and so tend to have newer chipsets.