For those who use Infuse and the QlVideo generator plugin and find that MKV (or other video) files are not thumbnailing, the following will fix it.
After installing QlVideo and Infuse (and running Infuse at least once), open terminal and run the following 4 commands in order. (The first command resets all filetype Uniform Type Identifiers, the second command clears the Quicklook Cache, the third command resets Quicklook and the fourth command kills all Finder processes and relaunches Finder):
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -kill -seed
qlmanage -r cache
Qlmanage -r
Killall Finder
All MKV files should now have thumbnails generated by QlVideo!