I found out that after changing the clip position the Alpha Tween as well as the Alpha final value are totally ingored. The clip is shown in the updated position but remains throughout in the Alpha setting of the first keyframe (even when it reaches the last keyframe which has a different Alpha setting). I verified that the Tween itself is executed by placing Trace statements at both keyframes. If I remove the repositioning statement, the Alpha Tween works fine (but of course in the original position which is wrong).
The problem is likely due to you removing the movieclip from its tween's frame of reference... a timeline tween involves position as much as any other property of the object. So if you change it's position you have dislodged it from that timeline tween scenario (expecting it to still do one part of the tween, but not any others). If there's some reason you can't orient the object where it is supposed to be, you should look into using an actionscript Tween instead.