It is very frustrating that Musical Fidelity was not able to identify the issue. If the audio from your Musical Fidelity M5si sounds distorted, consider the following troubleshooting steps:
Check Connections: Ensure all cables are securely connected and of good quality. Loose or unsuitable cables can cause distortion.
Speaker Polarity: Verify that the speakers are connected with the correct polarity (+/-) at both ends.
I had a similar issue with a Magnum Dynalab tuner The factory said the unit was perfect. I checked everything and discovered my power cord was causing the issue. I replaced the power cord and everything was fine. Maybe also replace your interconnect cable.
Taking the unit to your retailer is a great suggestion.