Is there a cable/sat box involved?
Ideally, that's what could partially solve this issue. Although HDMI/ARC is being marketed by various manufacturers, the better way to set up an AV system is with only audio/video going from various sources to AV receiver ("hub"), with audio signal going to speakers, and video signal passed along to HDTV/display. Audio back from the HDTV to Receiver still does not generally work well, whether you use HDMI or digital optical.
FWIW, sometimes Radio Shack has good deals on the entry level Harmony universal remotes. Second vote from me for that particular type of product.