Something to note here, the "Read Only" checkbox on folders has not worked since... Windows XP Microsoft Support Link However: "Note Unlike the Read-only attribute for a file, the Read-only attribute for a folder is typically ignored by Windows, Windows components and accessories, and other programs." So the Read Only attribute is ignored, and the checkbox is useless on folders.
Now with that out of the way, I THINK I may see what the issue is, however I have NO idea why this would suddenly stop working... I'll take a look on my end and report when I've figured it out.
AAAAAND 30 seconds later, the issue should be fixed. You'll have to remove any mods you've installed OR updated since yesterday, and reinstall them. This happened because I was getting ready to change how the installer loaded mod data, and inadvertently broke the XML it produced.