I would suggest that unless you require some really unauthodox shaped segments then you create new segments manually by using copies of existing segments. You can still use new .x file entities which have somewhat differing shapes to default ones and find no difficulty using the copies of the default scripts etc and new segment .x files so as to make new shapes as long as they are relatively roomlike pieces or other sensible wall segment shapes.
Making new segments this way is quite easy bypassing the need for the segment editor use which I would only use for completely new unauthodox shapes.
I am sorry but I dont personally know of the reason for your erronous segment editor behaviour.