Title kind of says it. When I import custom scripts they don't seem to be editable after a reload/logout, they are completely missing from the list on the left side...

Please provide some screenshots and ensure that other profile changes (whichever) persist.

All you're going to see in screenshots are the scripts there one minute and gone after a reload. Beyond that I uninstalled it and went with something else for now.

What about other setting changes? Do those persist?
you might want to verify that all your files in the WTF folder are writable and not set to read-only.