You appear to have compared what you heard on XP to what you heard on a new W7 system. There could have been differences in JRiver settings or Windows settings that affected sound output. In particular, you may have used a different output method on XP from the method you used in W7.
Probably. Or it could be a purely placebo effect.
FLAC and APE both decode, mathematically and provably, bit-for-bit identical to WAV files. You can test it (people have, even here on this forum), and it works. And, MC uses an intelligent buffering system to prevent any possible decode performance impact (with anything remotely approaching a modern PC), and if you go the full tinfoil hat mode, you can even set MC to pre-buffer the files to PCM in RAM before playback. Use FLAC or APE and you get:
* A modern, well-supported file format.
* 1.3-1.5x the storage capacity.
* Identical audio.
But...
Whatever. If it makes you happy, and you want to pay for the extra hard drive space it will require to store uncompressed audio in an ancient file format, then you can. MC will include tags for you (I would enable this if I were you -- MC can read them, so it is a good backup). Or you can turn that off and just trust the database, if you're a little on the loopy side. Make sure you store Library backups to a cloud backup service or multiple drives or something, and go beserk with your bad self.
MC doesn't care, and treats WAV as a full-class citizen.