This is true...the channels are reversed when bi-amping. It's strange but consistent. Simply switch your RCA cables at either end and it'll be correct. However, once you do this, there will most likely be a slight hum from the bi-amped fronts. It's barely noticeable (1' or less), but it's still annoying. I'm not sure if we're creating an internal ground loop of some sort, but almost everybody that has done this experiences this hum. But...it's very minor and not an issue unless you sit within a foot of the speakers. Either way, the bi-amp of the mains is such a big improvement and easy (relatively) not to mention FREE!
Jason