Hi Stefano,
I noticed that the hyperlink in the post
http://mydomain.org/downloads?nm=profile&mysecret=09ea99c0-b62d-14e4-916f-0440200cca66&nk={id}-{token}
is already changed when the email is saved to the emails table.
It becomes
{token}
In includes/module.php there is a line in clean_url_tags($text) that is responsible for this. If I comment that line out, the hyperlink is generated in the newsletter the way I expect it. From your comment I can see that it is there to clean up the url after the editor has turned it into an absolute url, but in my case the absolute url is intentional and should not be trimmed.
Best,
Paul