Common Mode Choke question
For a common mode choke to be effective all the supply current it passes through one limb of the 2 coils must return through the other limb of the coils. If your load also makes a connection to ground then you have, in effect, short circuited the 2nd limb of the choke and the common mode choke is no longer effective.

For this reason, it is better to isolate the load circuit from ground either by using a DC-DC converter or other methods such as opto-isolation.