For the user that is getting the "Enable Store Management" disabled automatically, open user properties in Active Directory Users and Computers and click the Attribute Editor tab.
Make note of the "Mail" Attribute.
Next search Active Directory for any users that have the same value for the "mail" attribute.
For AD object with the conflicting "Mail" attribute open Active Directory Users and Computers and click the Attribute Editor tab.
Find the "Mail" Attribute and change it to a non conflicting SMTP or remove the entry.
Give this change some time to sync then enable store manager and Login for for the user in question and restart the Archive Manager Active Directory Connector Service on the AM server.