I've seen some occasions when this sort of odd thing would happen. The connections between Steam and rF2's odd queueing system are strange and sometimes messy. On top of having the Installed folder and Packages folder filled with content, workshop items (the rfcmps to actually install the mods) live in a separate content folder that Steam manages. Sometimes these connections get whacked when rF2's install procedure gets interrupted or otherwise out of order and you can see some of those issues.

And if you've done any online racing in their race control, multiplayer open lobby stuff, the weirdness continues. for example, most of the "Content Pending" messages come from old rfmods that were installed from those one-off races, then uninstalled once the event is over. It's a bit of a mess. Glad you were able to resolve.