What if you press the trigger 1 less time than the number of segments? ...
... Also, how are you checking where each segment ends? The Text Overlay on the save settings window gives useful data about current and total number of segments and frame within the current segment, so it is probably the best way to check.
Using 1 less segment is the way I've been using this mode. I've been recording birds landing & taking off at our feeder. I make a mental note if the first segment I record looks expendable then I can make a decision whether to use the final segment if something better happens, not worrying that the first segment will be overwritten. I find this mode of operation good in this instance because although I have a remote trigger I still have to go to the camera to save when the segments are used up & it takes a while for the birds to come back.
I check the segments on the Play screen & the number of frames match my settings (except for the last segment).
Does your camera behave the same way in Segmented mode? If so, that would point to the software which I assume would be fixed in future and then I can stop spending time trying to figure this out.