Did you change the folders for your script mods?
Most of the script mods cannot be "deep" in folders. Rather than being able to put them all in a folder that says "Script mods" with a folder for each script mod within, the script mod's folder must be directly in the Mod folder.
Many times when people find their script mods aren't showing up, it's because they tried to "organize" things by putting them in folders with items that are similar (like all the toddler clothes in one folder, feminine adult clothes in another, shoes in another, wall patterns in yet another, mods like script mods, etc. in another.) It unfortunately doesn't work.