VC1 + AC3 problems

[velis]

I'm just remuxing my blu-rays.
That is, taking base movie stream, extract the VC1 and AC3 streams and mux them together into MKV.

I have two problems with this:
1. If AC3 stream is AC3 HD, Haali won't even detect it as audio. ??? I don't modify it in any way, so what gives?
2. If I mux a normal AC3 stream, resulting video will play fine where AC3 is decoded by ffdshow. If the same AC3 is passed through SPDIF, audio will break up and play intermittently at best (plays a few seconds normally, then does a few seconds pause, plays again, pause again...). Using ffdshow for both audio and video (wmv9 decoder for VC1)

What am I doing wrong here?

Note that this is not strictly MediaCoder problem since I don't exactly use MedaiCoder to do the remuxing.
I'm using just tsMuxerGUI and MKVMerge GUI to perform this "extraction".

I've never before had such problems with audio. Though before I always recoded video to H264.
I'm inclining to recode the video again, but it seems a waste since I'm quite happy with original 20GB video stream size (and quality).