Hi Scott - the main focus for joining curves is to form a longer closed curve that is made up of segments that touch end-to-end. Basically it wants to make a curve that traces out a single path from start to end.

So because of that it's only focused on joining 2 segments together at any single juncture point, you can't join together a branching structure where you have more than 2 curve segments all coming out from a single endpoint, which is what you have here for example:



So MoI's join just won't work for joining together a branching area like that with 3 different segments all coming off of the same point, you would need to something else like keep the pieces unjoined, or remove the dividing line so that the outer boundary was one continuous path rather than having that extra line down the middle...

You could remove the dividing line by selecting the parts, running Edit > Separate to break them into individual segments, delete the dividing line pieces and then rejoin the remaining pieces.

- Michael