Codec - A_MLP is Meridian Lossless Packing (see
http://en.wikipedia.org/wiki/Meridian_Lossless_Packing).
It's also known as DVD-Audio and Dolby TrueHD. Very common on Blu-ray discs.
You'll have to disassemble your MKV, convert the MPT to WAV or AC3, reassemble the MKV with the new audio substituted for the old, and run XenonMKV on the new MKV.
This program
http://www.noteburner.com/mp3-converter/audio-to-mp3-converter.html claims to be able to convert MLP audio. I can't confirm the claim.
Here's a decryting/encoding guide to MLP audio:
http://avisynth.org/mediawiki/DVDAGuideGood luck and report back on your success. (or lack of

)