You mentioned that Docking Station works. When you create a new world, there is a button to switch between a docked and undocked world. A docked world includes Creatures 3 and Docking Station. I'm wondering if you can create and load a docked world, or if you're only able to play in a DS undocked world.
Why are you deleting the files? That could be why it's not starting up: All of the assets aren't generated on the fly when it first starts up, at least as far as I know. Clearing anything out of the folders will likely remove necessary assets required to start the game. You can delete worlds from within the startup screen, but the only files I've ever deleted are those that I install myself (i.e. new agents, breeds, etc.)
If you installed everything in My Documents, there should be a folder for Creatures\Creatures Exodus\Creatures 3 with all of the files.
I've been hoping someone else will pop along with more technical knowledge, so apologies for the late reply! You might want to try one of the community forums, like the Discover Albia Forum
or Creatures Caves
. These are where Creatures players check in pretty regularly, and you might have some more luck in getting more responses. Sorry I'm not being of too much help, but good luck!
As I said I've tried everything. And yes, I can play both docked and undocked worlds, it's just C3 that acts up. By deleting files, I've meant deleting savedata/config/cache, not actual game files.