Well, its on you to properly troubleshoot. If the main out sounds fine and its only the headphone out that is lopsided, I don't know how Windows(or any other software) can cause that(unless the headphone out is being fed from a different source, like a send that feeds the headphone out, but NOT the main out). Also, consider that most every electronic device these days works fine...right up until it breaks
BTW, one system tweak that is almost universally required on a Windows rig is, go into Sound>Properties and make sure that windows is NOT using the interface as its default playback device(set Windows to use the computer's sound card). so maybe check this and see if it helps.