Magento – Transactional Emails modification

Even if I said something similar in the comments here it is as an answer, with some additional info.
When creating a module with a custom email template, the template is not supposed to appear in the custom template list. That list is only for the records in the table core_email_template. After installing the module the template should appear in the dropdown list when adding a new template to the database.
If this still does not fit your needs you can add an insert statement in the module install script that will add the same content to the template table.

INSERT INTO `{$this->getTable('core/email_template')}` SET 
    `template_code` = 'some_code_here', 
    `template_text` = 'YOUR TEMPLATE  CONTENT HERE',
    `template_styles` = 'custom template styles if any. if not leave null',
    `template_subject` = 'Subject here',
    `template_sender_name` = null,
    `template_sender_email` = null,
    `orig_template_code` = 'mycompany_mymodule_general_email_template', 
    `orig_template_variables` = 'custom vars if any in JSON format'

orig_template_code should be the same as the tag name in your config.xml file

Check you have files in app/locale/en_US/template/email

You should see files such as

• account_new.html
• account_new_confirmation.html
• ....
• wishlist_share.html

If not, then copy them over from a fresh copy of magento.