Both good tips. I just came across a link at AVS that also mentioned the new 981HD firmware.
The 990's remote was finalized before either HD format was launched, so if Sony is using a code set different from their DVD player codes it may be tough to find a code that will work. Keep in mind that when trying to progam in a DVD code on a button other than the DVD ("AUX") button, you'll need to specify that you want to use the DVD portion of the code library. See "re-assigning device buttons" on page 42 of the manual for the nitty-gritty details. That may not be the problem in your case, but I figured I'd toss it out in case it was useful to others.