Connecting the amp won't make any difference to this issue. You have something configured wrong in terms of bass management somewhere in the chain or you are listening in "direct" in 2ch stereo which would set your mains to large and may also try to remove the sub. If your mains are set to small, which they should be in about 90% of setups, this shouldn't happen.
What sources are you using and how are they connected and configured? Do they all do the same thing? Sending the wrong stream type may also affect this because the receiver is not decoding the correct stream type so you don't get true multichannel. For multichannel movies, stereo should NOT sound better than multichannel.