Check out that link I sent you. The dude's often talking about drinking beer 3 days after kegging, and that they're perfectly carbonated. I'm not saying that there must be some smart LHBS owners out there, I just haven't come across any yet. I hardly ever listen to advice from the ones I've been to.
You didn't mention, since you started this thread, have you tried warming up a problematic keg for a week, and then chilling back down and trying again? The reason I'm most convinced that it has something to do with your kegging process is that it's going away once you have bottled, and those bottles have sat at room temp. Chemical reactions happen much, much faster at room temps over fridge temps.
I say, on your next one, try 30 psi for 24 hours, then purge down to your serving temps, then wait 2 more days, and see what it's like. And don't shake. There's no way to be able to know how much co2 you're dissolving in by doing that. (And that's the part that also majorly differs between you and the process that brulosopher describes. he doesn't shake, and he's letting them sit at 30 for 12-24 hours less than you. all of that can add up to a big difference in carb levels). But also, if you didn't do such a great job at purging the keg, then you're also quickly dissolving in any oxygen that was present.
Also, here's a chart I like to use for force carbonation, instead of just guessing what it feels like:
http://www.kegerators.com/carbonation-table.php