First, let me tell you why this is happening: MC is a very precise player. When you have a 44.1kHz file, MC wants to play it for you at the native sample rate, or at a different rate that YOU specified in it's configuration. By default, it plays 44.1 as 44.1. Many FLAC files will be 44.1kHz, as they are sourced from CD.
However, many sound devices like bluetooth devices and some internal sound options (like your Mac's built in sound) can only play 48kHz audio. VLC is less precise. VLC just shoves the audio into the Mac's audio subsystem and let's it do whatever it wants. In this case, the Mac will resample the 44.1kHz audio to 48kHz and play it. All without you seeing it. But it's happening.
So, there are several ways to make MC play your files. Probably the easiest one is to set the option that tells MC "even if my device doesn't support the right sampling rate, convert it to one that works". Find that option here:
Tools > Options > Audio > Advanced > auto configure output on playback error > ON
That should do it.
Brian.