Understand, you are trying to connect a hodgepodge of different gear and use the soundbar (old, mind you) as a full fledged AV 'hub'. They are not designed to do this in the same capacity (and w/ the same huge flexibility) of even an entry level AV receiver.
You have discovered a conflict with your gear connections that a firmware fix will not solve. Time to finally grab an AV receiver on sale. I suggest buying a really basic one for ~$199 since they are perfect, and this would give you at least a year or two of warranty coverage. The speakers you could add over time, starting with (even used) fronts/center/sub, adding more over time as your budget permits. This way you can continue to enjoy the same audio connections you had previously.
If for some reason you wanted to grab something right now w/ surround and a sub, the Monoprice is a really inexpensive way to do it, and will still sound a lot better than your soundbar.
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I recently purchased a new Vizio TV (M50-D1) as a replacement for a Panasonic plasma TV I bought in 2008. I also have an Apple TV (4th gen) and Panasonic sound bar (SC-HTB10, from 2010) that I want to connect to the new TV (as well as a Tivo and blu-ray player). With the plasma TV, I had the Tivo and blu-ray connected directly to the TV with HDMI cables and the Apple TV connected through the soundbar with HDMI cables (the soundbar has HDMI-in and HDMI-out connections, allowing for HDMI pass-through). Audio out to the soundbar is achieved through an optical cable. The advantage of having the Apple TV connected as a pass-through is that since it's directly connected to the soundbar, I could mirror iTunes audio from my Mac to the Apple TV that was then output through the soundbar without the TV having to be turned out. I really like this setup, as I like to play music on the soundbar and I don't have a separate A/V receiver. In setting up the new Vizio TV, I tried to replicate this setup, but it doesn't seem to work. I don't have any trouble passing sound from the TV to the soundbar using the optical cable, and when the TV input is set to "Apple TV" with the Apple TV connected through the soundbar via HDMI it works just fine. The problem is when any other input is selected--such as the Tivo--the Apple TV seems to interfere with the soundbar somehow, causing it to not accept inputs from the soundbar remote (problematic, since that means I can't change the volume). It works for a few seconds, then the lights on the soundbar go out and a red light blink periodically, which the manual says indicates a problem. Audio is still coming out when this happens, it just doesn't seem to respond otherwise (except for on/off). This never happened under the previous setup. Any suggestions? I know this sounds a bit complicated, but I'd really like to get it to work out if possible. Thanks.