Why are some categories sorted by Tagalys Merchandising while others are not?

For Tagalys enabled categories, the Category sort order in the Magento admin panel is set to sort by 'Position'. In case, you have changed the Global Sort Option in the Magento admin panel for all categories to different sort order, the sorting of those respective categories will vary from Tagalys merchandising. 

In the event that this was changed on Magento, Tagalys will update the sort order back to 'Position' the next time an update is made (either manually or automatically) from the Tagalys dashboard.