since you never responded to the thread it eventually moved more than a few pages into the new threads listing where it was all but forgotten. since it has been many months it was also closed out by the staff (hence why a best answer was marked by the staff).
you may have gotten more responses if you had kept up with this thread by responding to posters.
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if all of your hdmi inputs appear when cycling through (eg... hdmi1, hdmi2, hdmi3) then you dont have any of them disabled in your menu
i'm not sure about what you're saying about autodetect being off but you could check out page 32 of your manual
http/ca.denon.com/DocumentMaster/US/AVR-590-OM-E_007.pdf which might be what you are referring to and might be worth looking at.
you say that you have your one device plugged into the "sat" hdmi port on your receiver but it only shows up when you select the "hdr" hdmi port?? what port is the one which seems to be working for everything? when selecting your input port it should only display when you have that particular port selected. eg.... it shows hdmi1 when you have hdmi 1 selected using the knob or hdmi2 when you have hdmi2 selected. it never should show hdmi1 when you're on the hdmi2 input with the knob... that would be odd indeed.
it could also very well be something is wrong with the receiver which may require service or you talking with the tech support/service people. i've had hdmi ports stop working out of the blue on the two receivers we have before. luckily they start working weeks later like nothing was wrong so i know something is amiss but its likely not hardware and is probably just the software acting up on the receivers. though it is possible for hdmi ports to go dead from hardware failure too.