Please help me fix my videos

You will be waiting a long time, then. WD’s attitude towards Twonky is that it is a third-party piece of software (it’s not written by WD, but bought in from PacketVideo, or whoever owns it now…), and even though it comes bundled as an advertised feature of the MyCloud product, they essentially refuse to support it in any meaningful way.

MP4 and MKV are entirely different, incompatible container formats; if you are renaming an MP4 file to MKV, you are doing it inappropriately. It you want to rename an MP4 video to an extension the may identify it as video, then the usual extension is M4V, although that isn’t an official extension of the MPEG4 standard.