There were some issues with modules that were resolved in HF3 or 4 I believe. I had problems with modules and importing/exporting them after I moved them in the UI tree. The child element had the incorrect parent element which could point a child to an incorrect parent or leave the child without a parent, thus causing the similar issue you're having now.
You might look at the element class data in the database and see if the node you're having problems with has the correct path and parent info. Also the only way I was able to resolve the issue I was to remove the UI node and start over.