How to Filter Very High Voltage Power Supply Noise
It may be that there is noise being coupled in from whatever is driving the system, I'm going to assume this is either a HV flyback or a voltage multiplier (and from the some od it, the multiplier seems mpre likely). Now when the switcher in the base turns on, it dumps all it's energy onto the stack in short sharp bursts (you get the same problems when rectifying AC feeding a big smoo5hing capacitor). Now at 10k ohms, your filter will allow A LOT of current to flow into your smoothing capacitor. Try either adding an extra cap directly to the output before the filter and/or increase the value of the resistor substantially (try 100k) and if that's still not enough, try (as Eric suggested) adding some large inductors to the output (start with something in the millihenry range) and see what happens.