Links to xerte actions don't work

Yes, the link is correct

Either check via management or direct in the database that the site_url and root_file_path and import_path are all correct.
In your case site url should be xerte.domain.tld/xertetoolkits/
root_file_path should be /var/www/xertetoolkits/ and import_path should be /var/www/xertetoolkits/import/

If that's all correct check the ownership and write permissions of the relevant directories especially USER-FILES but you should have checked and resolved any of that during the setup process.

HTH
Ron

Hello Ron, and thanks for the reply.

I've checked all the points you remarked in your post. Everything seems to be ok. I don't know where to look further.

I've also have an install of XoT2 (Available at xerte.ioc.cat/ ) Which works perfectly.

Compare the settings between the two installations and compare the directory permissions.
I know it doesn't help but this isn't a bug with xerte 3 code - there are many version 3 installations in use and I've installed and upgraded quite a few without problem. If your version 3 installation hasn't ever worked try dropping the database and running setup again being careful to check the prompts in each step.
HTH
Ron