https://sureai.net/forum/viewtopic.php?t=13560
I had this problem as well and managed to fix it.
This happens because the DSR patcher tries to read the Skyrim plugins.txt instead of Enderal's.
Note: If Skyrim isn't installed it will complain that the plugins.txt file is missing and prompt you to manually pick the file. In this case you can just pick Enderal's plugins.txt.
There are two ways to fix this.
Delete Skyrim's plugins.txt and manually pick Enderal's plugins.txt.
Copy the context of Enderal's plugins.txt into Skyrim's plugins.txt.
By default the plugins.txt file is located at C:\Users\USER\AppData\Local\Skyrim and C:\Users\USER\AppData\Local\enderal. If you are using Mod Organiser 2 you should look inside you MO2 profile folder for Enderal.