B sounds thinner

Is it more of a gut feeling or do you hear a clear difference, ie have you tried ABX?

A poor man's ABX would be to have a playlist with A and B only. Set playback mode to repeat playlist. Take a listen to A and B as you normally would.

Then close your eyes and press prev/next track keys randomly (those keys should wrap around the start/end so that more times up doesn't always result in A).
You're now listening to X. Decide if it is A or B before opening your eyes.

Problem is you cannot switch easily between X and A or B. But maybe JR MC has more advanced features you could use.

Anyway, foobar2000 can be set up bit perfect quite easily. Use WASAPI, ASIO, or even KS if you have to. You can set buffer times to whatever you want. It uses the reference FLAC library for decoding. In other words, there's no reason MC should sound different except if it isn't bit-perfect.

I always think J-River (on the Mac) sounds a little punchier/crisper than Pure Music.  I often wonder if they bump the level a little, but I've never measured to compare it.  The interface is still a little clunky on the Mac so I still find myself mostly using Pure Music.

Both use ASIO yet Jriver is consistently a little bassier and less forward in the upper mids. The difference is there whether I use wasapi, asio, or directsound as if theres a built in non defeatable eq in these players that give them their own flavor. I feel it may be somewhere in another stage of processing and not from the wasapi/asio/directsound stage. I don't know but I feel that these differences between media player's are bigger than the difference in your files.

EDIT: About the media players, It could be placebo due to the different color schemes between them hahaha. Can anyone else compare them to see if I am alone with this one?

I set F2K and JR MC up the same way (WASAPI, 24-bit/96KHz, etc. etc.). I MIGHT have had upsampling turned on in JR MC...or maybe both...or neither. I can't remember. That could definitely throw results off. Or maybe it doesn't make a difference with bit perfect? Either way, I thought I heard a difference similar to what you're describing. For me, given that I am no expert, the difference was small enough that it could have been placebo. I found myself gravitating towards JR MC in the end anyway, mostly due to the UI.