Hi Frederica,
if I understand your problem correctly, I'm afraid there is a major design flaw in your OM.
You have an Org-hierrchy with leader positions assigned to each orgunit and the "normal"positions also assigned to those orgunits. This is absolutely sufficient for the system to know, who is reporting to whom and standard reports, evaluation paths, structural auth., workflows all can be set up to work with this correctly. And this is best practise.
BUT you also seem to be using a position hierarchy in parallel. A position hierarchy is really only meant to be a quick and chaep alternative for an Org hierarchy, if you don't want to create orgunits. There is no new information in there. It's completely redundant. And your problem is proof for why this redundancy is damaging: you get inconsitencies.
I"ve seen this before. Whilst their might be good resons for it (I"ve never seen one), thsi is usually done by consultants, who don't understand orgmanegement or do understand that what they are doing is wrong, but rather have teh customer do double manual work with almost guaranteed inconsistencies than make an effort to properly understand struc. authorisations, reports or workflows. If you have no clue about OM, the extra position hierarchy can make some things easier.
So, my recommendation is:
1) check our, where the position hierarchy is used for reporting, workflow, authorisations or other things in your system
2) replace this by the org hierarchy
3) delete the position hierrchy (i.e. the 002 relationships between positions)