Jake:
Assuming you are using a mov or avi original file and you have checked to see if the Alpha lines up with the fill.
Also, assuming you are not using fill on one channel and playing the alpha on another, and if you are, then you have the two lined up.
A "cheat" work around would be start the expression to play.... pause (however many frames of black as you currently are doing it now).....then key the expression.
Just a way to keep your show clean :)
#Carbonite