Hello,
I just tested this on my local installation, everything is working as intended. When I'm writing a new e-mail and type the company name, I get the main e-mail as well as an entry from 'E-mail addresses" addon attached to companies.
How did you store the additional e-mail address for that company? Did you use the additional e-mails addon perhaps you added a new field to companies?
Kind regards,
Arek