Many thanks for the indepth analysis and the tests.
It would also be very odd that something would alter the signal only partially like you explained. Somehow something after MC's playback engine is causing the difference you are hearing.
I agree that it would be very odd if something is only partially altering the signal, though I have experienced a similar problem also with another prograrm.
Just to add more to the confusion, 32-bit 96kHz wav files I have upsampled to 32bit-192kHz using Cirlinka's HD-Audio Remaster 3.2 software (I usually upsample with Voxengo's r8brain) do not play at all on MC15 and produce only a high frequency hissing sound. The same files play perfectly well on Foobar, which indicates that there is no hardware issue at play.
It might help if you could list your exact output mode and DSP settings, volume settings (are you using the internal volume option in MC?), your OS and your sound device details. Also, you have not explained why you are using 32-bit files. How did you create them and what is the exact storage format? The output devices don't usually handle more than 24 bits (some drivers need 32-bit packages, but that is different, the DAC still won't process more than 24 bits.)
I will post details of my MC settings as soon as I am back at my home computer.
Now I only remember that system volume settings are at 100% and that I am not using internal MC volume settings. My PC is a Sony VGN-Z58GG running on Windows 7 Pro 64-bit with an internal soundcard. I do route my sound directly through a firewire 400 connection into a Brainstorm Electronic Distripalyzer masterclock and from there into an EE Minimax DAC with Sabre ES9018 32-bit chip that accepts 32-bit signals.
I am using 32-bit files (wav) as I have experienced that they sound better in my system than 24-bit files. So far I have only played back 32-bit 96kHz wav with MC (without any problems) as my previous DAC (Cambridge DAC Magic) did not accept higher than 96kHz signals. The new DAC accepts 192kHz input, hence my upsampling to 32-bit 192kHz which appears to cause the problem with MC.
More details on my MC settings will follow.