I suspect it's the Vsync setting, for the older ones I naively set it to be always on
but alas it works differently on every OS and GPU
(so in Zortch it's off by default and instead I hope that the triple buffering turns on in fullscreen, which is funnily enough the standard way to do it)
there are not many other differences engine wise
also recently Nekkrobox was updated , please check (sometime) if it still persists there