I'm also using the Harmony 650 remote to control the 976. I posted about the 976 remote about a year ago. The IR emitter is emitting slightly upward from the nose of the remote. That's just how it is for now. That's why you either need to aim a bit lower, or hold the remote in your hand so the buttons are facing either to the left or right. I've had great success doing just that. If the 976 doesn't "see" the beginning of the IR pulse, it can interpret the command as another function. I've seen this with many other remotes from time to time, back when I was involved in repairing many different brands. Of course, this is the first time I've ever noticed an IR emitter led not pointing straight out from the nose of the remote.
One thing I'm irritated about is, how long the 976 takes to turn on to an input. It's not 12 seconds, more like six to seven, but, I set my Harmony to the max delay for all of my activities. and it's still not a long enough delay. I'm always having to press the activity button again to switch the 976 to the right input.