Converting my CD Collection from .FLAC to .WAV

What transport and Dac are you using now? Which is burdened with the conversion and what processors are in the circuit? Depending on how the circuit is designed it may not handle this extra step without robbing you of something else (which you’ve eluded to). Are you only talking about digital downloads or previous CD rips? 

Digital downloads.

Jay's Audio CDT mk2 Transport

Denafrips Terminator R2R ladder Dac

Got it. You have nice equipment- should sound good. JRiver’s conversion to WAV is done in memory (as I’m sure you know) so as long as that requirement is met I don’t see it affecting your Dac. I agree that starting from WAV to begin with would be better as it eliminates the process entirely.

Another factor may be CD burn speed. Since music Cd's have traditionally been burned at low speeds to preserve data integrity, I reset the burn speed in Windows Media Player to "slow," and this has resulted in yet another layer of glare disappearing from CD playback. It is possible that the "fast" and even "medium" burn speeds that Windows is factory set to are too fast to guarantee absolute data integrity for music files. Of course, this also presumes that the flac files I am downloading were also recorded at a speed slow enough to preserve data integrity.

@bolong 

Have you checked any of the downloaded files with software like “Audiochecker” to determine the file provenance? Just a thought as some files are manipulated from lower resolution prior to being available for download or streaming. 
I’ve never experienced sound quality issues as a product of copy speed but then again its been almost 15 years since I used a computer to copy and store (used DB  Poweramp). I’ve been using a Naim Uniti Core for ripping/storage the last 5 years or so and have had no issues. Once in a great while a disk might produce ripping errors but the Naim will make multiple passes until it is overcome. I’ve never heard as much as a click during playback.