This has been happening to me for many years. It usually happens when I play a YouTube video and YouTube/MacOS sets my audio device to 48kHz. When I then use MC to play a 44.1kHz file, it sounds way slow and low pitched, because it's being played at 48kHz, instead of 44.1.
Generally, the "fix" for me is to press STOP on MC, which seems to reset things. I generally never use the stop key. Instead I use the Play/Pause key. I see no reason to use stop. I think this is why MC is not setting the sample rate. MC thinks it set the sample rate at the beginning of the song, so it doesn't bother to reset it when I "unpause" a paused track. But this track has been paused for minutes, hours, or days, and another program has reset the sample rate while MC was paused.
I guess one possible fix would be to reset the sample rate on every unpause event.
Brian.