PC games often have more variable aspects that can knock a good game's score down.
Something like no dedicated servers for online play will automatically guarantee a much lower score than the same console game that is commonly known to have P2P support only.
Scalability is another that can hurt a PC game's score. If the hardware requirements are excessively high relative to the complexity of the visuals, or if the low or recommended requirements result in a noticeably reduced experience even though PC games are typically reviewed on mid-high to high end systems.
Also, most games these days are designed with consoles in mind, even when developed on PC platform. Currently it seems that few categories like RTS or MMORPG are designed specifically with the PC in mind from the way the online play is set up, to the m/kb based controls. When you take a console oriented game and don't specifically tailor it to the strengths of the PC, that too can knock the score down in a reviewer's eye.