Problem

By default, Magento shipment emails are sent without tracking numbers. This is because the Magento API requires a two step process. First we create a Shipment for the order, and then we add the tracking numbers to the Shipment. Unfortunately Magento sends out the email after Step 1, but before Step 2.
 

Solution

The missing tracking number can be fixed by telling Magento not to send the email until after the tracking number has been added. Follow these directions to set this up.
 

In the Magento Admin Panel, go to System > Templates > Transactional Emails
 

1. Sometimes it is under System > Transactional Emails
2. Click the Add New Template button at the top of the page.
3. For the Template option, choose New Shipment from the pulldown list and click Load Template.
4. Enter a new unique Template Name like: New Shipment after Tracking
5. Click Save Template at the top of the page.
6. Repeat steps 2 - 5, but this time choose New Shipment for Guest as the Template.
   
   
   
   
    
7. Now go to System > Configuration
8. Click Sales Emails under the Sales section.
9. Select the Shipment section to expand it, then set the Enabled option to No.
10. Select the Shipment Comments section to expand it, then set Enabled to Yes.
11. For the Shipment Comment Email Template option, select the first template you setup.
12. For the Shipment Comment Email Template for Guest option, select the second template you setup.
13. Click Save Config at the top of the page.
    
    
    
    
     
14. After this, Magento will only send shipment notification emails to your customer after the tracking has been uploaded to the system.