Exactly because of this I resample everything to 48kHz by SOX highest quality in Foobar and JRiver. But still analog seems to be better to my ears. I also tried to switch resample/no resample and don't hear big difference. Much lower than A/D.
Even bigger difference is playing from simple Linux player bootable from flash disk to ADI2 DAC. This is even better than from Windows. It is hard to explain why but it is so. If I want the best playback, I use this
wtfplayer with DAC. Operating system+player together around 20MB. Only WAV, FLAC, DSF files.
By the way there is another difference between analog and digi input - use of internal (a) or external clock (d).