Is it feasible to chain high voltage dc boost converters together to get bipolar (dual) output rails?
It turns out the problem was due to interaction between the two converters via the link joining them (positive output on one to the negative output on the other). When I tried filtering the output previously, I only added components to the +/-HV rails and not the shared ground. Adding ferrite beads between the converters and ground got rid of most of the noise. Thanks everyone for their suggestions, they helped steer me towards the solution.