It turns out that the noise is either injected through the EOMs or through some mechanical oscillation in the table or through RFPD SN020. The servo card was working normally. However, since I had opened up the box, I used this opportunity to increase the first stage gain on the FP2test input and also made it 50-ohm input impedance by adding a 51 Ohm resistor in parallel to R8. Now, beware that on the actual board, R5 and R8 labels are actually swapped. This helped keep the gain set by AD602 to 7 dB now, instead of 30 dB maximum. This way we are able to increase the gain more instead of getting saturated. The hunt for 500 Hz bump would move to finding on table sources now.