Secure pages breaks databse updates with update.php

Secure pages prevents the system from running the necessary database updates.

When running update.php the system tells me I have x database updates, it all runs smooth and drupal tells me the database has been updated, no errors in watchdog, except the database changes were not made. Running the update.php again shows me that the same issues are still ready to be updated.
Disabeling secure pages, running update.php and then re-enabeling secure pages works just fine.