The Extender Discovery Tool only works if your RFX is in Network Mode and you switch from position 1 to position 3 while the tool is running.

Assumption here is that you are using PEP1, PEP2, or PEP3.

When you Add Extenders to Project, that is only the first step. For PEP2/3, the next step is selecting (Clicking on) the 'Component' containing your IR codes for the equipment you want to assign to the Extender.. Now, on the right hand side of the Building Blocks Area, you will see all Extenders that have been added to the project.
In your case, you'd want to ensure that Extender 0 is checked when you have 'DVD', for example, selected. Finally, select IR Port from Building Blocks using the drop-down underneath the checkbox area (initially will show IR Port 1).

If you are still having issues, email me at the address on my profile and I will send you the Philips PDF that was used for the Pronto Certification Program (2MB) that should explain things a bit more.

Lyndel