Hi Steve,
If 'Remember Form Options' is enabled in User Preferences, then the previously used Email Cover code will be remembered for the next emailing, rather than being blank. This is done by document type, so an email cover used for sending invoices will not be remembered when emailing credit notes or order confirmations. The cover code is remembered concurrently for individual printing and for range printing from the Order Entry menu.
There is no company profile option for setting a default email cover.
Default email covers can be set on Customers, from the Invoicing tab.
I expect that this process might differ in other modules, due to the way settings are remembered.
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Regards,
Softrak Tech Support