Hey there @frein!
First thing to know is that the Navigation Bar has its own Active / Hover color that is separate from the main Foundry Control Center's link controls. That being said, what you're seeing seems strange with the footer if you have the Control Center set to Lighten. In my tests I do not see this same behavior.
Here's a short video showing a link in a Paragraph stack as well as the link in the Footer stack. They both act the same when set to Darken or Lighten for the link hover style:
http://d.pr/v/4KkNSY (see updated video below)
If you will post a link to a ZIP file containing your project file I would be glad to take a look at it.