Filing an email in Salesforce which is being composed is slightly different that filing an email which has been received.
When Track with ZynBit is clicked, the message changes to say "Enabling ZynBit email tracking" meaning that tracking will be enabled.
Regardless of the tracking option selected above, the email can be filed to the contact, company or any other object using the Quickfile lightning bolt icon or the A -Action File Email option. Note that the email files immediately when the icon is clicked so it is best to complete edits before filing the email.
Once the email is filed, the checkbox will be visible on the envelope icon, and a green confirmation will briefly flash stating that the email has been filed.