Windows Media Player and Media Player Classic: To remove or disable the unwanted subtitles, simply disabling it within the media player does nothing.
Go to the Codec folder Start>All Programs>eg CCCP or K-Lite>Filters
Select VSFilter Configuration
Click on the General tab
Select Do Not Load in the Loading section
Click OK
Go to the Codec folder Start>All Programs>eg CCCP or K-Lite>Filters
Select FFDShow Video Decoder Configuration
Click on the Subtitles box on the left sided menu to uncheck/deselect/disable Subtitles
Click OK
VLC Media Player: Do the 2 above procedures and within VLC Media Player, while playing each MKV video, right click on the video and select Subtitle Track>Disable