When we set up our API Role, they did not have the permissions either.
The "fix" seems to be to create a new API Role and the permissions will show.
Then just assign that new API role to your existing user.
Here's the solution we got from Marketo support:
I figured out the issue. It looks like we introduced 4 new permissions in the June release and one of them is "read-write campaign". However, if you go edit the existing role, these new permissions don't show up for you to select. If you create a new role such as the test one I created called "Mkto Support Test Role", you will see 4 new permissions available.
To get around this issue, you will need to do the following:
(1) Create a new API role with the extra permissions you need
(2) Assign the new role to your API user and remove the old role
(3) Delete the old API role if you don't need it anymore.