Are you using WASAPI or ASIO? If not, pretty sure the Windows Mixer is messing with your bitstream - check your settings and try one of them if they're available. The difference should be readily audible. Caveat: I'm not a computer expert by any stretch, just going off my personal experience.
Ok, I'm willing to give anything a try. So I went like this –
I took a number of songs which I'm familiar with, some in flac 44.1khz and one in flac 96khz (I changed the sampling rate to 96 before listening to this one of course). On one hand there is Winamp going through windows mixer to Schiit Modi, from there to Arcam rHead and finally to Audeze lcd2c. on the other hand, Adobe Audition going straight to the Schii Modi using ASIO. The switch between them is just pausing one player and hitting play on the second.
I switched back on forth using all the songs. Didn't notice any difference. I did noticed obvious difference when I re-engaged my APO equalizer and listen to the songs through my custom curve for the lcd, and that really made the most improvement