This is not the impression we want you to have when using QuickBooks, QBFrustrated. 
 
QuickBooks Desktop has a sticky setting feature that remembers the previous information you used for invoices and will continue to use that information unless you change it. The Auto-check the 'email later' checkbox if the customers preferred delivery method is email feature ensure that invoices will be set "email later" for all customers that want invoices to be emailed.

Since it doesn't apply to all the new invoices, let's try opening a sample company file to check if you're having a problem with only one file and not the program itself.
 
Before doing some troubleshooting steps, let's make sure QuickBooks Desktop to the latest release and you meet the system requirements.

Here's how: 

1. In your QuickBooks, go to the File menu at the top left.
2. Choose Close Company.
3. In the No Company Open window, click the drop-down arrow in the Open a sample file icon.
4. Choose a sample file and click on it.

Then, try turning on the Email Later feature and create a sample invoice.

If it works, it's possible there's a damaged data on your company file preventing the Email later option to automatically show in the new invoices. Just run the Rebuild Data tool is built-in to fix any company file data issues. 
 
You can check out this article for the steps and details: Fix data damage on your QuickBooks Desktop company file.

 
If the same thing happens, we can open the invoices and manually tick the Email later option. Then, contact our Technical Support Team. They'll pull up your account in a secure environment and investigate what's causing this issue.

Here's how to reach them:

1. Click the Help icon on the top menu. 
2. Choose QuickBooks Desktop Help. 
3. Tap Contact us.
4. Select Search for something else and enter your concern in the Tell us more about your question: field. 
5. Tap Search. 
6. Choose Start a Message or Get Phone Number to connect with our support. 

Visit our Sales and customers page for more insights about managing your customer transactions.
 
I'll be right here to continue helping if you have any other concerns or questions about QuickBooks. Assistance is just a post away.