Connections are:
Direct TV (ARC port) -------- HDMI ------> Vizio TV -------- HDMI ----------> Samsung Home Theatre
Does the Samsung Home theatre have any networking capabilities? If yes, are they disabled? Likewise for the Vizio TV.
Edit:
Here is a link with respect to Samsung:
http://www.samsung.com/au/support/skp/faq/1039760
I understand that your TV is a Vizio but the link does provide some insight with respect to HDMI and ARC. Do you have the Vizio User Manual/Guide?
I am wondering if there is some handshake delay taking place between the devices. At start up tries to "connect" somewhere and then, thereafter, no longer attempts to do so.
Are all of the HDMI cables ARC? To be honest I am not sure about how some mix of HDMI cables would create the problem you are experiencing.... Will mull that over some and in the meantime perhaps someone else will add a suggestion or two.