There is no audible difference between Windows Lossless and FLAC. None. Zip. Zilch. Anyone claiming to hear a difference is making things up.This is absolutely correct -- these codecs are indeed lossless. It may be possible that there are some products or software out there that screw up the decoding/playback processes to different degrees . . . but there is absolutely NO sonic degradation associated with these file types. They also both support high-resolution sampling rates and bit depths.
But they do behave very differently in terms of the metadata, FLACs are supposed to use Vorbis tags, and WMA lossless files use a propritetary tagging scheme . . . both of these are different from the ID3 tags used for MP3s. This may affect how easily you can take the files between various playback platforms and still keep them organized in the way you like.
So I would recommend that you decide based on what is best supported by the software and hardware that you wish to use for organisation and playback. And since they are lossless, you can transcode between formats with no loss in sound quality, if you ever need to.