I'm having almost an identical issue. This is my setup:
TV: Samsung UN50EH6000 (lower version: not 3D, not smart TV. Otherwise quite similar)
Receiver: Pioneer VSX-521-K
Samsung Blu-ray player: BD-E5700 (lower version)
I have each of the three components hooked into the receiver with HDMI, and the video is output to the TV from the single "HDMI output" from the receiver to one of the HDMI inputs on the TV.
My apple TV and my Motorola cable box both work fine. I have had this receiver for almost a year, and I have never had any issues with these two components.
The Samsung Blu-ray player is new. It works fine when playing Blu-ray disks. However, I have noticed that when I am simply playing DVD's, the video cuts out after several minutes (usually less than 10 minutes), but I can still hear the audio. I even tried changing the video output setting on my Blu-ray player to a constant 1080p (Instead of auto) , but no luck. The video still cuts out after it plays for a little bit.
The Blu-ray player plays dvds perfectly when the video is hooked directly into the TV, but there is not a digital audio output to get quality audio to my receiver.
This issue sounds identical to the above post. Any advice, either from the above poster or from a new reader?
Thanks in advance