OK, so I changed out all the cables and still have the same issue. I changed the HMDI out to a different out and even changed to a different HDMI on the TV. Same issue.
I again hooked up the Apple TV right to the same TV and have no issue.
Brought down another tv and ran from Apple TV to pioneer to tv and had the same issue but not as bad. It seems like when there is a new item on the screen (volume icon, Netflix icon, changing apps eat..) it blacks out. For example when I turn up the volume the bottom right corner has a volume level graphic (made by the receiver) the screen goes black and then back on again. Every time I turn the volume up or down it will do this.
When I go from the Apple TV to the tv there are no issues it seems to only happen when the it runs through the receiver.
now the cables I used today were ones that I had in the garage that were extra, I would not think it has anything to with the cables, but I could be wrong. Very frustrating with this new expensive Pioneer receiver.