Geoffrey_Coram
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You have to realize that Cgs and Cgd are *not* two-terminal capacitances. That means that Vd has an effect on Cgs, even though the drain is not directly connected to the "capacitor" Cgs.
The way BSIM3 is formulated, it computes the total inversion charge Qinv as a function of Vgs, Vds, Vbs. Then, Qinv is partitioned to the various terminals -- depending on the parameter XPART, you could have Qs getting 100% and Qd getting 0%! Obviously, this is not physical, but it is a limitation of BSIM3, not the simulator.
Cgs and Cgd are the partial derivatives of the gate charge (which is usually -Qinv, and the partitioning doesn't come into play); note these are different from Cdg and Csg (where partitioning does matter).
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