The hookup that you are using is not correct for hooking up a 6-wire motor to a G540. The G540 is designed to handle 4-wire motors (or 4 of the 6 wires of a 6-wire motor). You should not be connecting the center taps to a positive voltage source. Rather, you will want to hook up "half coils" or "full coils" to the G540, and tape off the extra wire from each winding.
There is a gecko document that illustrates the two different wiring options - Look at Figure 9 and Figure 10 of the following document: