If you have the latest CoreAVC, it must have come with Haali splitter.
If not, get it (it's free) and install it.
Then change the registry so that VMC recognizes MKV files as video files
Windows Registry Editor Version 5.00
Save as a REG file and apply (i.e. execute). MKVs will now work in VMC.
From what I read (can't try) this doesn't work with 64-bit Vista.
Some claim simple renaming MKV into AVI will do the trick (Haali must handle AVI as well).
It is not a question of being able to play, but making Vista Media Center recognize MKV as a valid video format and use the proper codecs.
VLC has its own codecs, uses nothing but them and doesn't share them...