I worried about this as well, as it was the one real negative I've read about the 9000 remote. My solution was the teach the remote the navigation commands for the directional pad and then teach the transport commands to some of the buttons about the macro buttons. It sounds really strange, but it works out pretty well for me.

The programming problem with the remote sounds odd. I did struggle some figuring out how to get punch-through to work (mis-understood the manual for some reason -- it made perfect sense when I re-read it a week later). If you have problems again later, you might try posting what you're doing to see if anybody can spot a mistake.

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gonk -- Saloon Links | Pre/Pro Comparison Chart | 950 Review