Just bought my very first processor, the 990, along with an Anthem amp. Its an upgrade from my prior system, my alarm clock. Mated them with 3 new polk speakers, and I have no complaints on performance! The remote though, touted as being "intuitive", has some quirks that don't make sense to me. The volume buttons should work irrespective of which device is selected to be controlled by the remote. The volume should simply always default to the 990. After all, its a sound system being controlled and it is reasonable all attached gadgets will rely on the 990 for sound control. Also, selecting the 990 by pressing the "TNR" button prior to selecting the input source seems unnecessary. Finally, the manual says other remotes can teach the universal one the codes used for their particular device, but I didn't see those instructions detailed anywhere. I relied on the scrolling through method where power button and source button are alternately pushed until the device to be learned is turned off.

Curious about DVI; is it inferior to HDMI in any way except for no audio signal?

Do yourself a favor and look into either Universal Remote Controls or Harmony.
I have a URC MX-850 and I love it.
It is easy to program & has IR/RF capabilities and you can find these for about $180.00 or so on the internet.
Gonk has the MX-900 and has a very nice review in his signature.

Now that is one heck of a jump!
It can - the feature is called "punch-through" and needs to be turned on.
It's necessary because those input source buttons double as other functions when controlling other devices. Unless you move to a third-party universal remote that does some macro functions, this behavior is nearly unavoidable.
I haven't read through that portion of the 990's manual in a while (years, actually - my 990 remote went in the drawer within a couple days of getting the 990). The 990's universal remote has a large code database in the back of the manual and can accept other codes not listed there (Hi-Fi Remote maintains an extensive list that will work with the 990), but it doesn't support learning commands directly from other remotes and it doesn't support macros.

My wife still says that our first good universal remote (the venerable MX-500 ) was the best upgrade we ever made - better than HDTV, surround sound, separate amplification, or Blu-ray. Like butchgo, I'm a die-hard fan of URC's remotes (although I still rankle at their short-sighted policies about distribution of software). The MX-850 that butchgo uses is functionally almost identical to my MX-700 (just a different color, different navigation pad, and RF support). Personally, the MX-900 is my favorite URC remote among those I've owned, and it can be had from Surf Remote for a very reasonable price.

One potential benefit for the Harmony remotes is the fact that they are geared for consumers and not custom installers (URC doesn't like to admit that normal consumers represent any sort of customer base for their higher-end models). As a result, the software is designed from the ground up to be easier to use. The flip side is that you sacrifice some direct control over how some of the nitty-gritty details (like macros) behave in the process.
Nope - HDMI's video spec was lifted almost piece-for-piece from DVI. I've got some details about both HDMI and DVI in my sig - click on "HDMI FAQ" to see that.

Also, when talking specifically about the 990's DVI switching, we are talking almost solely about what the plug looks like - you can switch HDMI through the 990 to HDMI displays just as well as through a standalone HDMI switcher (possibly even better, as I've had problems with at least one HDMI switch that my 990 has never given me). Some people have even been able to switch HDMI audio through the 990, but I'm 99% sure that you need to have dual-link DVI connectors on both HDMI-to-DVI cables or adapters to achieve that.

I'll chime in on the URC MX brands. Like gonk I started with an MX-500 went to a MX-700 and finally went to an MX-850 for the RF and love it.

I can do anything I want on the 990 with the URC remote.

Thanks for the info guys...gals?

The source buttons don't have any soft-key labels next to them, so I didn't realize they can have other functions.

Will look for the "punch through" function. Remote is otherwise programmed. Will do some reading and get a blueray player then possibly look into other remotes.

I only got my 990 4 days ago. While I was waiting for it, I hooked up my amp to my computer so I could control the volume. I played some mp3 music files, and noticed a huge deficit in sound quality compared to using my cd player as source (required manual switching of input cables on back of amp).

Well, after I hooked up the 990, it was like a magic wand took away all the badness from the mp3 files, especially the low bitrate ones. Now my mp3 files sound nearly as good as my cd music. Does the 990 edit the digital input from my computer, filling in gaps as it were, before relaying the signal to the amp? or is it something else?

It's most likely the difference in your sound card's DAC and analog output stage and those of the Model 990 - major difference in quality of parts and design. Had you played a CD in your computer rather than your CD player, I suspect that you would have noticed similar issues.

I have the Harmony ONE and it is without a doubt the best item I purchased when I upgraded to the 990/7125 combo. It is easy to program and can run any macro you can think of to make it do. It also error corrects by asking you questions about the system. I labeled each of my components the same way I named them in the remote and I haven't gotten any more of those stressed phone calls at work about why something isn't working. It takes about 2 minutes to explain to someone how to use it and the rest is in the software. Don't struggle with the supplied remote and trying to learn it a bunch of codes. The Harmony website (Logitech) has all of the codes for all of your equipment, and it all works flawlessly. You actually program the remote on line and the website saves your settings. You can edit any time you want and add or subtract equipment. It will be the last remore you ever have to buy. You can even set it up to control multiple systems if you wanted.

My 2 cents...

URC remotes are far more durable than the Harmony remotes. While I like the looks and layout of Harmony better, I became tired of having to buy a new remote every 12-14 months. My URC has held up like a champ, and you can program in the error correction.

I haven't used any Harmony remotes, but I've still got very URC remote I've bought since 2003. The MX-500 in particular has been dropped countless times, knocked off furniture by cats, spit up on by an infant, and splashed with water in the kitchen over the last 5.5 years. Aside from the backlight not working anymore and some wear on the case, it works as good as the day I unboxed it. The MX-700 looks brand new after 3.5 years.

I don't have jester's experience with both Harmony and URC remotes but I replaced a Harmony 880 with the Harmony One not long ago. Several of the buttons on the 880 gave out after a couple of years. I will say the Harmony One is much nicer remote with a touch screen, better buttons plus I think it is a better built remote than previous one-handed Harmony models. Regardless of which universal remote folks use I think most find it a terrific addition to their HTs. And it is always a plus when the rest of the family likes it too!