I just looked this up as I am trying something similar. It appears to me that the use of equations between parts in assemblies does not work if one of the driving dimensions is controlled by configurations.
For a simple example.
I have two parts in an assembly called 'Box' and 'cylinder'. The length of the box is set to equal the length of the cylinder by an equation. However, If I then create a number of configurations of the cylinder (controlling its length) and then change the configuration of the cylinder used in the assembly, the square will not update (or at least I can't get it to) - Has anyone come across this before? Anyway around it?