I'd suggest calling Logitech and explain the volume control issue you are experiencing. On the rare occasions I've had to call them (I have the Harmony 880) they have been very helpful. They should be able to diagnose the problem and reprogram your Harmony 1000 while you are on the phone with them. They will take the time to allow you to test it to see if the revised programming works. Let us know how it works out.
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AvFan
Outlaw 976 | ATI 2005 | M&K 850s Left, Center & Right, Surround-55s, MX-70B Sub | Harmony 950 remote | Panamax 5100 | OPPO UDP-203 | LG OLED55B7