From the AP-Pack you should copy only the "AP\Weather" in the Assets, for other routes just when they have a specified folder for the route, for Berlin Leipzig, IKB3 are no such folder.
Do you have other standard routes, copy in there just the specified folder for installed routes.
I did myself the following, first renamed the Assets folder to Assets0, then I installed the Enhancement Pack, the new Assets folder I removed from the TS Installation, and moved it into another drive, so I can see, where the Pack is installing himselve.
I supose that you installed the pack, whitout nowing where it comes in. ist maybe installed also for routes what you do not have.
No you can do that what I did, rename the Assets folder temporarely, remove the new Assets folder, containing just the Enhancement Pack, in a secure place, than rename again the primary Asset folder.
Now you can see in the new installed and removed Assets folder, where the Enhancement Pack is installed in your Assets, now you can search installed Assets, for routes you do not have installed, and remove them, that would hopefely help to resolve the issue.
How I could see on my PC, the Enhancement Pack comes also with an scenario for the Midland Mainline London Bedford (00000034-d000-0000-0000-000000002014), if you have this route, you can try the scenario, if you do not have the route, you must delete this folder with this scenario in it, can make issues.