Arria II GX refclk pins

Well we are talking about clk pins (not user io). They have to be set as lvds by somebody. Physically you have connected the lvds pair, but it is not clear what you have done in HDL interface itself when declaring the clk. There is some tool inconsistency here. depending on your tool I believe you should try and declare only the positive signal in your entity, you may then get false warning about the negative pin but ignore it.