You don't mention how your equipment, including your TV, is connected together. The symptoms you describe are often noticed when there are separate connections run from the player to the TV and from the player to the receiver. The TV's video processing is taking less time than the receiver's audio processing.
If you can, you should use one HDMI cable to connect the player to the receiver, and one HDMI cable to connect the receiver to the TV.
You also don't mention where you have configured the audio decoding to be done -- in the player or in the receiver. For testing, at least, you should try enabling the audio decoding in the player. The player should properly delay the HDMI video to correspond to the audio decoding delay. Set the player's Digital Output to PCM. See page 39 of the player's manual.
Marantz SR7009 avr + MM9000 amp --> Atmos 7.1.4
Fronts=NHT 2.9+AC2, FH+TM=DefTech PM1000, LCR+TM amped