Hi There,

I was having the issue too when changing the phone number through the account settings.

To bypass it, what I did was:

View an invoice - click the gear icon - click the "change what your customers see" link.

When the invoice editing window comes up, select "Content" then the pencil icon for the invoice header.

Here you can enter the phone number, in the format you want without Quickbooks inserting the country code.

Hopefully this helps, someone!