I've been setting up my new VSX-1021 today. It's been a pain but I think I finally got my inputs configured right. Part of the problem was that I tried to use the provided software, "Wiring Navi", to do the setup. Wiring Navi is a wizard and I made some mistakes and had to backtrack several times. Then I still don't think it applied all the settings right. It went much smoother once I opened the receiver's OSD menu and setup through that.
Here's a couple tips that may help someone else.
The AVNavigator software apps (includes Wiring Navi and others) run within a browser. But they did not run within Chrome for me. I had to make IE my default browser before launching the apps. The apps use some ActiveX control so you have to click in the message bar to allow the control to run.
I used I wired connection to connect my receiver to my network. AVNavigator could not auto detect the receiver. I checked my router and the receiver did get an IP address via DHCP just fine. I opened the Settings page from AVNavigator and was able to manually enter the receivers IP address and then the Pioneer apps were able to connect to the receiver. I think AVNavigator's auto detection feature is just broke.