Quackling

So this is weird... (Its always something weird with me)

02 Lancer LS, all stock. At idle, in neutral, all is good. Put it into drive (or stop at a red light) and the idle gets rough, enough to vibrate the car. Step on the gas and drive, and it runs just fine. I thought it was due to the drag from being in gear, and the idle dropping too low, but the tach doesn't show any noticeable drop. Maybe a tiny bit, but that could be my imagination.

Then it got weird. I noticed that if I put it in Reverse, it doesn't do it; idles fine. Which makes me wonder if it's somehow a transmission thing...? Automatic, btw.

I had a problem several years back, with really rough shifting. That turned out to be bad input and output speed sensors. Replaced them with used ones form the Wrecker, and problem hasn't come back. Could that be related? I don't really see how, but there it is.

Tune up procedures have had no effect on the issue. I got a slight improvement by snugging the slack out of the throttle cable, but I think that is just holding the throttle open a tiny bit, more a band-aid than a solution.
I've tried disconnecting the battery so the computer could relearn how to run it, but the exact problem comes right back.

I broke down and asked the shop to diagnose it, and they said they couldn't find anything wrong with it.

What should I be checking for?