Eh, I'm pretty sure they're still going to get the close calls, at least when they play us. I'm a firm believer that the slight disfavor of the Bills by the refs has everything to do with psychological bias. I think they're reinforcing an image that they believe (we are no good), and when something is a close call, they err on the side of the better teams.
With the Patriots, we've seen them get some bad calls in the past (a Carolina game comes to mind), but I think the larger bias is against teams that are thought to generally be bad.