You are both right...
Ray is right: putting chokes on wiring coming out of the machines blocks high frequency noise generated internally by the machine by by oscillators, switching of transistors, etc, which would otherwise become a radiated EM issue, causing said device to fail EMI certification.
Mactec is right: adding chokes on signal wiring (like USB) prevents the signal wire from becoming an antenna to pick up high frequency radiation coming from the machinery that Ray failed to protect properly
. Choke provides the impedance to block high frequency signals while passing lower frequency and DC.
Back to the OP: he is having problems when a large induction motor cycles on/off. Think this is an EMI issue, or a brown-out issue?
I don't think a choke would solve this, because we aren't talking about high frequency noise here, where a choke is going to do you the most good. This is looking like a one time pulse, which will probably make it through the choke.