Oops forgot about using rf id 10. The way I mentioned doing it will work, but the other way is the correct way to do it.
I also can't say that I have run into any of the other issues that you are having. But I will say that whenever things just don't seem to be working like the way I programmed them that many times it's the result of rf interfernce.
Are the antenna's just flickering after you hit a button on the remote? I would check to make sure both of the antenna's aren't flickering when your not sending any codes to them. Sometimes you have to look at them real closely, the flickering can be very subtle. You might need to repostion the antenna's a little more. If you do have a lot of interfernece I would suggest trying the "I" version of the remote and antenna's, but if your an end user and not a dealer that's not very easy to do.
You might also try adjusting the ir output level for the SageTV. There are trim adjustments on the top of the MSC400 for each ir device.