My observation is that FLAC v. WAV sounds different when both are local.
I would expect them to sound different, especially when local. As others have reported (including you), I also have a preference for WAV. I also find FLAC more variable.
WAV is generally (not always) non-compressed. It was developed by IBM and Microsoft and is the 'preferred' format for Windows. Since the Taiko Extreme is Windows based, this may be a contributing factor (among others) to WAV file superiority and preference (by many) as inferred by final sound quality vis a vis the Extreme [as reported in this thread].
FLAC is cross platform and open source with open implementation (READ: variability) not to mention the complexity: frames, compression / decompression // encoding / decoding, algorithms used, etc., ...despite "perfect reconstruction."
I expect that ANY well implemented audio system with high levels of transparency can and does differentiate between file formats. What is preferred by the individual audiophile is another matter.
-----------------------------------------------------------------------------------------------------------------------------------------------------------
Note re. FLAC [from Wikipedia]: "The amount of compression is determined by various parameters, including the order of the linear prediction model and the block size. Regardless of the amount of compression, the original data can always be reconstructed perfectly.
For user's convenience, the reference implementation defines 9 compression levels, which are
presets of the more technical parameters to the encoding algorithm. The levels are labeled from 0 to 8,
with higher numbers resulting in a higher compression ratio, at the cost of compression speed. The meaning of each compression level varies by implementation.
FLAC is optimized for decoding speed at the expense of encoding speed. A benchmark has shown that, while there is little variation in decoding speed as compression level increases, beyond the default compression level 5, the encoding process takes up considerably more time with little space saved compared to level 5."