Well after a few hours of messing around with things, I think I have it sorted out.
The HTPC works fine when plugged directly into the TV, so I started to focus on the receiver. I noticed when making changes to the settings of the receiver, and it would reset itself so the new settings would take effect, this cleared up the artifacts and screen flickering. So I figured maybe I had to start my HTPC up first, and after about 10 seconds or so (as long as windows is starting), I then turned on the receiver and it started just fine with the 1080p, 60hz settings on the desktop. I was previously starting the receiver first, and then turned on the HTPC.
I guess the receiver needs to see a signal input for it to start correctly, no idea why, but seems to work consistently now.