MKV files not playing

I first installed kodi16.1 as an optional package on retropie on my PI3. I connected it to my nas and was able to play all videos including mkv files without issue.

I then installed kodi16.1 on my other PI3 with the raspbian OS. When I now load up kodi on raspbian, mkv files will no longer load or have major buffering issues.

Has anyone experienced this issue? Any reason why kodi on the retropie build would perform better than on raspbian?