Can you manually Send Email on an order when MageMail's order confirmation email is enabled?
The way that the MageMail order confirmation email works is by disabling the Magento order confirmation email in the System > Config > Sales Emails section. The manual Send Email button also relies upon this setting and if it is disabled will not send the order confirmation email manually.
Here's the trello card for the feature request to allow manual order confirmation sends:
One workaround that you can use meanwhile is to temporarily re-enable the Magento order confirmation emails, send the email, and then disable again. Note that this will send Magento's standard order confirmation email and not the MageMail one.