How to transfer MKV file from Windows PC to iPad Mini
Do not bother with conversion. Install the free video players like VLC or PlayerXtreme and upload the videos via wifi directly to the apps.

EDIT: Alternatively, and also must faster for large files, both apps allow transfers via iTunes. If you don't use iTunes read on...

For example, once installed you enable Wifi Transfers...

  

Then from your browser you go to the address shown and upload the files...