Given the fact that only administrative users have the ability to add companies, I suspect the cause of this is an orphaned record in the table which maintains company security.  Most likely the company security still contains a reference to the sample data company folder from a previous server, and because that server has been decommissioned you can no longer see it from the company list window itself.  The resolution of this will probably require contacting support who can use a Company Editor support tool to confirm whether or not this is the case, and clear it out.

Given the fact that only administrative users have the ability to add companies, I suspect the cause of this is an orphaned record in the table which maintains company security.  Most likely the company security still contains a reference to the sample data company folder from a previous server, and because that server has been decommissioned you can no longer see it from the company list window itself.  The resolution of this will probably require contacting support who can use a Company Editor support tool to confirm whether or not this is the case, and clear it out.