remote has nothing to due with this issue.
it does it with the stock shield remote.
Gotchya 
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it also a usb RF remote....the only IR it has is for TV power button only. so media commands are via RF.
The way it's sent doesn't change that though.... It's an adjustment that can be made in Harmony remotes and some equipment is done via BT, IR, RF or IP.
Odd indeed.....