A moot question at this point since you're no longer using the Squeezebox ecosystem, but do you remember if the Squeezebox settings were configured to stream FLAC natively? And just curious, what did your measurements reveal?
My measurements showed just a few things that made me think the fidelity wasn't 100%. First off, the S/N ratio when playing a computer generated sinewave as it came out of my preamp (thus using my preamp's DAC) was nearly 6dB lower than the same track burned to a CD played on my DVD player through my preamp's DAC. I also did a computer generated frequency response sweep and found the Squeezebox exhibited the start of a roll-off above about 18kHz while the DVD player just started showing roll-off at the edge of my measurement gear at just below 20kHz. They should have been identical, so my perceptions in the blind listening comparison tests were supported by the measurements suggesting one or the other was not truly reproducing exactly what was on the original file. Since there was much discussion online about the likelihood of transcoding on the fly with the Slim Server, I assumed it was the Squeezebox platform which was lacking the full fidelity. But I didn't pursue it because I really wanted that platform for non-critical listening of music throughout the household and I was fine with loading a CD in my main high end rig.
As for the settings, I tried everything anyone online suggested and while sometimes those settings broke everything - including a couple full uninstalls and reinstalled with all fresh setup choices - and I never got any better sound than my initial setup.
I don't do FLAC as back in the day it was VERY questionable and at that time I was ripping everything either with a fully-licensed (and quite pricey) professional Fraunhofer MP3 Variable Bit Rate encoder or Windows Media Player's WMA Lossless. My library was already about 2,500 CDs worth of content in those two formats, so going back and starting all over with FLAC (after the initial kinks were worked out and the lawsuits stopped) wasn't an option for me. I remember a few times reading online that Slim Server was incapable of streaming either of my formats, so if that was true, and I had no reason not to believe it wasn't true, then I could never listen to my huge library in native format anyway. I was okay with that once I exhausted all my attempts to make it right after about 6 months. I just lived with the idea it wasn't perfect and enjoyed my music around the house and on my rear porch.
That was my experience with the Squeezebox platform.
Once some core capabilities I had come to enjoy went away, the other annoyances grew more annoying, and Alexa started playing all my music plus pretty much everything else I could ever want, I gave up on Squeezebox altogether. If anyone wants them, I think I still have two of the original players and remotes. One of them is even Slim Devices branded.