A couple of ideas.
First of all, Premiere Pro does support MKV - at least, it does in version 13.0.2 (though I’m on CC, which you may not have the benefit of). Update if you can, and it may solve your problems.
If you really do need MP4s, transcoding is a pretty wasteful way of doing it, both in terms of time and quality. Far better would be to demux the audio/video streams from the MKV and then remux as an MP4, provided you aren’t using video or audio formats that are illegal for that container.
I tend to use ClownBD for demuxing (it’s a nice frontend for eac3to), or you may get MKVExtractGUI to work for you. Once you have the discrete streams, use MyMP4BoxGUI to reassemble it as an MP4.
If that isn’t working (because of some format issue with your source), try tsMuxer to make a .TS file - this is a pretty accepting container, especially in terms of audio, and Premiere has supported it for quite a while.
Hope that’s of some help!