Make sure the custom scenery is listed in the log.txt first. Then, check the scenery_packs.ini file in the Custom Scenery folder for them.
The file has the following rules:
- Packs are loaded in order of the file – the first pack in the file is the highest priority.
- When X-Plane runs, it removes from the file any packs that are missing. (If you delete a pack, the list is auto-updated.)
- When X-Plane runs, it adds to the top of the file any new packs it discovers that are not listed (in alphabetical order). So if you install new scenery, it is installed at highest priority.
- If you delete the file, the file is completely rebuilt, as if all packs are new. You should probably never do this.
So, you can edit this file to make sure they have a high priority and show up over any default scenery. More info available here
(it says X-Plane 10 but still applies for 11).