There is a bug in notes for companies. You have to correct two things:
1) On 'application/controllers/CompanyController.class.php' on function 'edit_client', around line 227, you will see a list of company properties. You have to add 'notes' to the list, like this:
...
'phone_number' => $company->getPhoneNumber(),
'fax_number' => $company->getFaxNumber(),
'notes' => $company->getNotes(),
2) On 'application/views/company/add_company.php' around line 167 change $contact_data to $company_data, like this:
<?php echo textarea_field('company[notes]', array_var($company_data, 'notes'), array('id' => $genid.'profileFormNotes', 'tabindex' => '185')) ?>
This will be fixed for next release.