It sounds like you seriously need a Combat Management Program.
Combat management program? meh.
There are two things that make 4e combat long: analysis paralysis, and lack of preparation. A computer can't fix the first, and isn't necessary to fix the second. (Okay, 3; but MM3 has mostly fixed the grind.)
4e forces you to make a lot of choices round-to-round. Tactical positioning is actually important; focusing the party's attacks is actually important; deciding when to drop that daily is actually important. Some people FREEZE UP in that sort of situation. One of the people I play with, and we've been playing the same characters together for over a year now, is just starting to get over this.
In 3e (and this gets worse and worse the further back you go), you didn't have many (rules-system-supported) choices to make during a fight. When it was your turn, you made your attack roll if you were a martial character, or you looked at the 2 or 3 biggest spells you had and fired one off. If someone had severe analysis paralysis problems, they played a martial character (and suffered, alone, during character creation).
Now, even a relatively low-level martial character has a half-dozen things, USEFUL things, they could do. If you're the kind of person who loves turn-based strategy games, you'll say it's awesome. If you're not, you'll say that 4e ruined D&D by making it play like a board (or video) game. And if you love turn based strategy games but are playing D&D with an analysis paralysis sufferer, you'll say that combat takes too long in 4e.
A computer changes nothing here.
Now, preparation. You talk about loading all your monsters into the program, about loading all the characters into the program, about tracking their initiatives, whether they've used their powers, and what conditions are on-going, all with the program. And that's great... but you can do the same thing with enough sheets of (variously sized) paper.
Monsters? Write (or print) out the stat blocks onto a sheet of paper, with a generous margin. Characters? Write out power cards, and keep them up-to-date. These things take time, but so does entering all this stuff into your program. Someone already mentioned the "initiative stack" of index cards; I've also played with little name-tents (like, business-card sized pieces of paper, folded in half, with the name of the character or monster), that you put in a line, and some sort of token representing whose turn it is. For conditions, as DM, you should write out a card for the precise effect that any monster can dish out; don't use generic cards ("where are my 'immobolized's") always make new ones. When the PC is effected by it, hand them the card. Auras? Leave the card on the table, by the creature generating it (have the aura size be a nice big number everyone can read clearly). When the PCs effect a monster, yeah, you could write it in that generous margin on your monster sheet; or it'd be faster if you took the power card the PC used and just put it by the monster sheet, or by their name-tent, or by their mini; whatever works for you, but set some table-rules and be consistent! (Admittedly, multi-target effects can become difficult; shuffle the monster sheets into "effected" and "not" groups. Thankfully, in practice, having multiple disparate sets of multiple monsters being effected by multiple different save-ends powers is rare.)
Oh, and never erase. Erasing is a time-killer. The tiny hp box on the default character sheet is a JOKE. And when a monster recharges a power, don't erase the 'X' you put by it; draw another 'O'. (It sounds stupid, but seriously, try it. DM in pen.)
How much time do you waste going "Hey, did you hit with that power last turn? Is this guy still slowed?" or "Okay, you're slowed... someone dig out a marker for that. Orange? No, orange is being used for dazed. Umm..." Things slow down when you try to keep it all in your head, or when you try to make reminder-tokens on the fly. A computer is one way to fix that problem. But you can also do it by preparing, and liberally using, paper.
I spend 40 hours a week programming infront of a screen. I don't want to do any more of that during D&D.