I have the same problem. The error is different depending on which directshow filter I'm using:
1) with coreaac: MC hangs. The contents of the analysis window is completely white. The contents of the main MC window no longer update
2) with ffdshow: analysis stops but MC is still responding. However, while playback still works for new songs, any further audio analysis is impossible. I get the error 'audio analysis needs files on a locally accessible drive' or something along those lines. Everything else seems to keep working, after restarting mc (killing it is not necessary) analysis works again.
It is indeed always on a random file that the error happens, no matter which directshow filter is used.
I have tried this with haali media splitter as well as mp4splitter. (though I'm not sure how to tell windows to use a specific splitter when both are installed)