Unlike the permissions required for issue and item synchronization, check-ins require additional permissions in custom access personal access tokens to synchronizer check-ins.
Since these permissions are needed so that the synchronizer can access the ADO API correctly, if they are not added to the personal access token or a full access token is not used, the feature will not work.
The permissions needed are:
Code - Full
Graph - Read
Project and Team - Read, Write & Manage
Symbols - Read
Work Items - Read, Write & Manage