AnkiHub doesn’t sync deck settings.
The issue can happen if the deck has different “due numbers” or positions. The positions usually correspond to the creation date, so that older cards have smaller numbers, but this is not always the case and Anki has a feature to reposition cards. One solution to use this feature to sort the positions:
- Open the deck in the browser and sort by the Created column.
- Select all cards then click the Cards > Reposition option.
- Leave the default options as shown and click OK.