I'm using the latest build of MPC-HC, 220.127.116.1148. But I experience the same issue with the latest "official" build, 18.104.22.16847. I even experience when going back to the last official build, 1.4.2499.
As for chapter skip, how do I do that? These are single-file MKVs, not DVDs, so there are no chapters per se. Using the dedicated fast-forward/rewind buttons in the controls has the same effect as clicking ahead on the seek bar. The act of moving ahead to a future part of the video, no matter how I do it, makes the video and audio play faster.
Somehow the problem seems to be wrapped up in how the audio is decoded. As I mentioned, if I let MPC internally decode AC3/DTS itself, everything is fine. But if I try to passthrough/SPDIF the AC3/DTS to my receiver, then I run into these speed issues. Any reason why that might be?