I just finished a game in DGS, and by my view, I feel like I should have won this game on account of all of the dead white stones in the center and upper side. Is there something about DGS that I don't understand in regards to scoring? Does it not count dead stones into the score? Do I have to manually tell the system that those stones are dead? I'm seriously confused. Looking at it with the SGF file attached, the game didn't count a lot of territory at all. Where are the rest of white's corners? Black's upper side?

You have to mark the dead stones manually. Here is the detailed explanation.

Aw. jeez. Thanks! I had no idea. I wish the app told you something like, "please mark dead stones" after the game is finished. I assumed the program did it automatically.

The program does not know.

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Still officially AGA 5d but I play so irregularly these days that I am probably only 3d or 4d over the board (but hopefully still 5d in terms of knowledge, theory and the ability to contribute).

Computer programs are not always able to correctly identify the life/death status of groups, and some are better than others. Some programs/servers do not mark stones at all and you have to do it (e.g. DGS apparently), some will automatically mark what it thinks is dead and you can then modify this to correct the mistakes, or if you are a jerk to cheat (e.g. KGS, OGS), others use the computer-decided status and you can't change it, so tough luck if the computer is wrong but there's no scoring cheating (e.g. GoQuest, new Tygem client?).

Good to know, thanks! I see no sense in cheating the system in online go. Would it really make someone feel better to cheat to say they won when they know they didn't? Seems silly and doesn't improve your game at all.