Just upgraded? Then things to check:

1. Permissions on all the folders in the xoops_data folder are CHMOD 777
2. Update the "system" module in modules admin
3. If you had the Protector module installed before the upgrade then update it in modules admin
4. If you didn't have the Protector module installed before the upgrade then use your FTP client to delete the module from the modules directory (some people have reported this as a bug).

Is everything working alright apart from this?

Sorry, I did do all of those things.

Here's the weird thing:
I had the PM, User Profile, ThAdmin installed.
I uploaded Oledrion, and that's when I noticed the issue - id didn't show up to install. So I removed marquee, which was the last mod I installed, and IT shows up under available mods, but not anything else. I then uninstalled PM and IT disappeared as well.

Ok, so here's the update.

I disabled protector and everything worked. I reinstalled all the mods, re-enabled protector, seems to be working, however, I lost the "protector" button in the left navigation of the admin - it never came back.