FPGA velocity estimation and VFD noise

Hi, I'm using an NI FPGA (a 7411, I believe) with an RT unit and VFD to get very low lag, high resolution velocity estimation from a 3600 pulse/rev quadrature encoder (mounted on the VFD driven motor). When the VFD is off and I turn the encoder by hand I get very good tracking and low noise. With the VFD enabled, however, the system is very noisy and usually has about a 1-5% error. The whole system needs to have as little lag as possible (<.01ms).
I'm looking for ways of reducing noise in the system programmatically on the FPGA or of enhancing the noisy signal to make the system more sturdy.

Can you change the switching frequency on the VFD?
Is wiring to motor in conduit? Is conduit metal? If so is it grounded?
Failing that, many cable manufactures now offer armored cable designed just for VFD applications they may reduce radiated emmisions compared standard thre phase cables.

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