I'm very familiar with a *similar* behavior. It may or may not be what you are reporting.
Sometimes, I'll play back a file with a sort of high sample rate: Say 48kHz. I'll pause that file for some time and then when I return I decide to play something else with a sample rate of 44.1kHz. So I double click and it starts playing. But the playback speed is wrong. It seems that when paused and a new file is started, the DAC is never told to switch sample rates. So the DAC is stuck at the old sample rate and my newly played file sounds too fast.
In reverse they would sound really slow. Like if I paused a 44.1kHz file and then doubled clicked a 96kHz file. The new file (if the DAC does not change) would play REALLY slowly.
I've had this happen dozens of times in the last 8 or 9 years I've been using MC. The solution is always very simple: Press stop. Press play. Fixed.
Again, this may or may not describe your issue.
Brian.