Actually that particular behaviour of segments happens with default segments also - it has nothing to do with user made segments in particular as far as I can ascertain.
I make very few wall type segments as theres no need to do so in most cases - a straight wall for instance is just that so no point in makeing a new staright wall. I just chamge refs to textures in most instances. I dont change any of the 16 part segment refs.
That behaviour occurs sometimes with me in joining walls in only a small number of situations when multiple joins of the same segment show no occurance one out of many suddenly shows that behaviour - it could be one of many touching and joining over the same or numerous heights. Its an erratic occurance - and not constant so is not missing corners as the if that were so all such corners would be missing when they arnt. Yes FPSC does not recognise the corners and drops them out when they exist - it just clips some away.
It seems to be and almost certainly is be relative to building using both external and internal walls where corners meet. Whatever - once the behaviour occurs its very difficult to overcome as FPSC is not easily fooled or overidden and it embeds the info it sees useually for good sometimes leaving a run of wall segments all of which are perfect corners and then one which stands out like a sore thumb with a bad one.
But yes its corner pieces are the problem - you could check to see is the corner elements are missing in script but where it occurs with me they are not. I only use copies of default scripts for element pieces in standard wall shapes and they still behave occasionally in that way.
At least thats what I have found to be the case.
Most erronous or issue probs with segments like texture inheritance cant be overidden by the user they are editor governed so only TGC could solve them.
It could be of course that you do have corners missiing in your new segment set up - I am just saying that it can also happen with default segments too.
There are other similar things that occur with segment use e.g. if you build a room and put a top (floor) on it and go above and stand on top of the roof you see that the floor or roof whichever way you describe it does not fit to the edge of the walls in a similar fashion. Corners are not fashioned in this situation either as in use for a flat roofed building. FPSC does not accommodate such by default.