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Problem: Active Directory Synchronisation - System Tree Sorting

I installed a new ePo 4.0 server a few weeks ago. Most of the installation went fine but there are still a few issues I would like to solve. And the most annoying is the system tree sorting.
I am probably doing something wrong because I searched the whole forum and found nobody with the same problems;

I want to manage 2 domains from this ePo server, and they are both synchronised on Active Directory (2000 domain).

So I created a new system under my organization, lets call it Domain A.
The settings for this domain are:
- Synchronize: systems only (as a flat list)
- Move systems from their current System Tree location to the synchronized group

Under Domain A I created 2 groups; Servers and Workstations, and at both I selected "Systems that match any of the criteria below (IP addresses and/or tags)"

For Domain B I did exactly the same.

Now when I synchronized for the first time all system where directly under the Domain and not in their intended groups. I already found out that this is because of the sorting status that has to be enabled.
But when I enable that and sorted all systems again the workstations from Domain A are where they are supposed to be but those from Domain B are also under Domain A. Same with the servers.
Why does he do this and can I do something to keep them in their own domain?