I just got a DIRECTV HUGHES SD-DVR40. I previously had the 950's remote programmed a DIRECTV HUGHES GAEBOA receiver, and then a Scientific Atlanta Digital cable box (I used the SAT button to program the cable box buttons in.
Now when I press the SAT key, it flashes quickly again. It didnt do that before.
I have tried clearing all learned codes, and tried having the 950 remote learn the DVR's keys but I am not having much luck at all. SOme keys learn, some dont etc.
Any suggestions by anyone having a similar problem?

I'm afraid that I haven't ever run into this. Did you learn the codes for the Scientific Atlanta cable box's remote to SAT without entering in any code, or did you re-assign SAT to use cable box codes and give it a code for Scientific Atlanta? It's just a guess and could be way off base, but it is possible that if the SAT device is set to accept cable remote codes, some of the Hughes commands could be hard to learn. If you haven't done so already, you might also quiz Outlaw Tech Support . Also, I'll offer a suggestion that I often give 950 owners - the 950's manual is a pretty good resource for the included remote, but Universal Remote also has a pretty large remote manual dedicated to it that can be really handy.