I'm saying that you should tween using AS.
A workaround would be to have the instance named, say, 'box_01_mc' in frame 1. Set it's alpha to whatever you like. Then when the tween starts, make sure that the instance name you are using is different than the one you set the alpha on. (box_02_mc) THis way, Flash is seeing 2 different instances...but to the user, they are the same...