I have a mainmenu module in the right moduleposition that has 3 menuitems. When I click any of the menuitems, the menu disappears and everything else seems fine.
When I disable the joomsef the menu works as intended(it doesn't disappear).

Hi,

This seems like the wrong Itemid is being stored with the URLs. This happens when you have more than one menu items pointing to the same component or article, and JoomSEF chooses the wrong one to store. Open Menu manager in Joomla and find the Itemids for your three menu items. Then go to Manage SEF URLs in JoomSEF and check the Itemids stored with the URLs for the menu items. If they differ, edit the URL and change it.
Clear the JoomSEF's cache after the changes.

Best regards,
ARTIO Support Team

After purging SEF urls it started working normally. Glad it didn't happen on production site...