Hi Nico,
Most of the switchmode power supplies are not grounded, i.e. the postive and negative DC outputs are floating. Just look at the mains connector of the power supply, most of them only have two pins for the AC and no pin for the earth.
So grounding one side of the power connector via the USB ground should not create a ground loop.
By the way, I have been too busy with work to do any more testing of the PWM TEC
Hopefully soon