i wonder if mm is running at 16bit internally. i would think that could maybe cause clipping in the signal path.
also i noticed some bog audio modules caused clipping for me. the bog umix one has a soft/hard/none clip setting in vcv, if you right click on the module in vcv(i dont believe the alt settings for modules are available to choose on the mm itself).
but im guessing maybe your clipping is coming from somewhere else in the patch.