I added this block to my advancedsettings.xml:
<video>
<override>
<adjustrefreshrate>
<fps>25.0</fps>
<refresh>25.0</refresh>
</adjustrefreshrate>
</override>
</video>
It seems to come from this thread and yields no results for me. The video is still output at 1080p50hz.
Interestingly enough I just watched some 25Hz and 30Hz (at 1080p60hz) material and did not notice any frame skips. This is with mediacenter 17.8-098. Maybe it is fixed in Kodi 18?