I have some sympathy with you lurkingman. My husband and I have very different sleep patterns. So we both just go to bed and wake up when we want to. Sometimes our sleep patterns coincide, but there's no way either of us would expect congruous bedtimes.
Having said that, I think he found that quite difficult when we first got together. For him, going to bed together was one of the things that identified us as a couple. But he's less rigid about it these days!
On the other hand, my brother is a computer programmer and it is also his hobby. He gets home from work at around 6 and then is back on the computer programming until 1 or 2am or so. He's quite often up again at 4 and gets a few hours in before work. But it is the sort of hobby that is all consuming and computers literally do eat time (as I'm sure anyone who has spent an hour or two too long on MN during the day can confirm!)
I know that my brother spends a lot longer than he thinks he does on his computer. In the daytime, he's often late to things or has to cancel at the last minute because he hasn't left himself enough time to get there because he just needs to get this last thing finished. He says the same as you, that once he's in 'the zone' he doesn't want to leave.
Neither my brother or I sleep 'well' and we both feel as you do, that a little sleep leaves you feeling more energetic the next day. Although computer use late at night does leave your brain over stimulated and less able to shut down too.
Sooo...
Is your wife controlling generally?
Does she feel that she doesn't see you?
Do you have young children and she craves adult (your!) company?
Is it simply that she misses you and feels really strongly that although you are there, you are not actually there?
I suppose the crux of it for me is, is she placing an unnecessary amount of importance on you going to bed together, or is she just desperate to spend more time with her husband?
Could it be the case that you spend more time on the computer than you think you do, but less on it than she thinks you do because you're both living under the cloud of "Is she going to nag me to get off the computer/Is he going to be on the computer all night again?" Which focuses both of your attention on the quantity of time you are together, rather than the quality.