Do you have multiple P3D discovery locations for your add-ons in P3D? This could be the reason why it is being added twice. I would try and look if you have multiple entries in your scenery.cfg which has two files locations if I recall correctly.
In terms of the warning, I suspect but you need to check, is that when you navigate to your FSDreamTeam Exclude folder, the tool you are using I believe is checking for a .bgl being present in the folder. If there's no .bgl in the scenery folder it will likely generate this warning.
I have this symptom too, but I use a different tool which also shows me the same warning. I ignore it.
The Exclude folder will be empty unless you have created a specific exclude file (.bgl) for one of your installed sceneries for GSX Level 2 via the FSDT GSX Control Panel.
