My 06 WRX has this same issue an it pisses me off. Everything is stock except my invidia g200 cbe.. as far as I know. Bought car at 73k in june, now at 91k.
I took it to the stealership an tried to get it to do it but for ONCE it didn't do it.. but its worse the longer you drive.. an it only does it in 2nd when using the gear to slow the car..So when I am going to have to stop at a light or traffic, I throw it from 3rd to neutral or push the clutch an stop from 3rd.
Has any one yet figured it out? I found this thread through google..