Or, "why does every catalogue I install eventually break?"
TL;DR: Install GOG's Creatures Exodus directly into My Documents and everything will be fine. Be really frustrated by this pointless requirement, because it's frustrating.
Alright, so. Games on Windows were simpler in the 90s and early 00s. Windows hadn't ever enforced its multi-user environment the way other OSes of the time did, and consequently few programmers coded any per-account disparity in settings or 'addons' in their software. Windows XP started to introduce user accounts as a 'thing' but didn't force it; Windows Vista and its successors were progressively sterner.
Permissions on files were being tightened version by version, and older applications might have to demand administrator access just to run, since many traditionally kept all their configurations and so forth together in Program Files, which isn't typically 'owned' by any user. Every Creatures game exhibits this traditional behavior.
Back to GOG-- I don't know where they got it, or how they built it, but someone, either Good Old Games or whoever had the engine before them, tried to modernize Creatures Exodus. They forced it to split its files between Program Files-- the base files that the game comes with-- and My Documents-- all the creatures you export, the agents you install, and so forth.
In theory, this isn't bad; if you don't have an administrator account on your computer, after all, you'd be completely unable to play otherwise. In practice, it didn't work at all, and breaks in new and exciting ways every single time I encounter someone who's encountered the issue.
No, the Creatures Remastered patch doesn't fix it for everyone, if it fixes it at all.
No, changing the directories in the config files in the Docking Station and Creatures 3 directories won't fix it. They'll just be rebuilt by the engine next run.
The most common and immediately noticeable fallout from this is catalogue errors. Catalogues are glorified text files where Creatures 3 and Docking Station stores its help files and other metadata (like quirky cookie recipes), so the game accesses them frequently. Almost any catalogue error will halt the game, and worse, the engine is very picky about there being no duplicate catalogue files. Guess what having two Catalogue directories in two different places tends to do.
Install GOG's Creatures Exodus directly into My Documents and everything will be fine. Be really frustrated by this pointless requirement, because it's frustrating.
I got sick of doing this, so I install from an ISO rip of a retail Creatures 3 disc and then smack Docking Station on top, and then spoof the C3 disc so it lets me actually load docked worlds.
How much time do you have and how low is your bullshit tolerance?
If you have the time, just reinstall the entire game into My Documents.
Otherwise, read the errors, check both the directories, try to consolidate files and address duplicates, and pray. The next time you inject a new agent, you will probably go through the exact same process.