For years, many audiophiles have pointed out that WAV and FLAC sound different even though the files contain exactly the same samples. One hypothesis is that the extra CPU processing (although small) required to uncompress FLAC adds noise or jitter that somehow affects performance of the downstream DAC.
To test, convert one of your albums from FLAC to an uncompressed format (WAV or AIFF) and compare to what you are hearing from Roon. Let us know if this change narrows the gap between Roon and USB thumb drive or DLNA playback.