Wrong term assignment

If I can resolve these one or two issues, this modules will be a life saver...thank you, in advance.

Now the meat:

I have a multiple-hierarchy tree, weighted at points, etc. I created a new article, and hit 4 checkboxes for 4 different terms (none of them, just so you know, had multiple parents). The resulting article had only 2 terms applied to it - the 4th that I had selected and then another term that I hadn't selected.

The only commonality between the other three is that they are parent terms. So it looks something like:

Grandparent
+ Parent <= Selected
+ Parent <= Selected
+ Parent <= Selected
+ Child <= Selected <= Applied
Parent
+ Child <= Applied