I was looking into why muxman doesn't like DTS-MA Core DTS audio. It seems that the standard DTS frame rate is 2013 bytes. DTS-MA core DTS frame rate is 2016 bytes. Other discussions on DTS-MA Core audio discuss the having extra frame bytes. I can't 100% confirm this but here's another program that has DTS issues.
DVD Studio Pro will reject DTS files that are not formatted correctly.
One reason DTS files may not be accepted is because DTS encoders produce DTS streams that contain a frame size of 2016 bytes as opposed to 2013 bytes. This is an incorrect frame size and therefore will not be imported into DVD Studio Pro.
So what to do. Getting Muxman to fix the problem in their free version is not likely.
Another approach: Disguising DTS audio as PCM audio.
I took my DTS audio file and changed its file extension "file.dts" to "file.raw" and imported it into Audacity then exported it as a wav file. "file.wav" All this does is put a wav header on the DTS audio. When this is Muxed to DVD the header is removed and your back to Standard DTS. Muxman has no problem with this DTS wave file. It treats it like standard PCM audio. After making my DVD I still have the problem of the audio thinking its PCM. This is where INFOEDIT come in. I open the dvd in INFOEDIT and change the audio properties back to DTS audio. Save the new .ifo files and DVD knows it has DTS audio and plays back perfectly.
For those of you that have some problems using AudioMuxer with DTS-MA Core audio files this is the work around I have found.
Huckamazoo