When Marketo sends emails, you can think of building the email in 2 steps:
If the {{token}} value is www.domain.com, that would be expected to not track because of the above 2 steps. After the {{token}} value is inserted, Marketo does not go back to wrap tracking code around http/https. The {{token}} doesn't look like a URL when the system applies the tracking code because the tokens don't pull the values in until the next step after.
The solution to tracking tokens is to place or on the outside of the token, like such:
{{token}}
That way, when Marketo builds the email, in step #1, the system recognizes the http and knows it's a URL. Then the tracking is wrapped around the http and the {{token}} as well. Then in step #2, the {{token}} value is inserted into an already-wrapped link.
Keep in mind is that if the {{token}} value contains http, but http is on the outside of the {{token}}, the link will break. Let's say the URL you want to insert is www.domain.com. You have to move the out in front of the {{token}}, but you don't want to also have it inside the {{token}} as well or your link ends up being http://www.domain.com.
To get around this, you'll need to remember to take the out of the {{token}} value.
{{www.domain.com}}
would instead be
{{www.domain.com}}