Hello,
Companies, much like other RecordSets like Tasks, Meetings or Contacts, can have certain e-mails attached to the record and have these e-mails displayed in the e-mail addon.
When you archive an e-mail, it's attached to Contacts (both sender and receivers). However, it is not attached to either of the Companies. And also, when viewing the e-mails addon in Company, you are looking only at e-mails that are specifically attached to that company, e-mails attached to contacts that belong to this company are not displayed.
If you'd like to have a certain e-mail displayed under the company, it's possible to link any e-mail archived in the system to the Company. There's currently no way to display all related e-mails to a given company.
Kind regards,
Arek