Hello @TheKeeper20 ,
This sounds like a Microsoft Outlook problem, not necessarily a Quickbooks problem. The setting in QB Desktop for sending mail through Outlook is a single radio button so there are no settings within QB that are likely to solve this problem for you. This is a known problem for some Outlook users and usually occurs when you have your email account set up as an IMAP email, as opposed to POP or Exchange. Here is a good resource to troubleshoot that issue:
https://www.slipstick.com/outlook/email/two-copies-of-sent-messages/
If that isn't your issue, then there are a number of troubleshooting steps that you can try to alleviate the problem:
https://social.technet.microsoft.com/Forums/en-US/616a6f33-730c-40b4-af5e-f5984982595f/outlook-sends...
One that I can see being a problem is the Send/Receive interval conflict during Send/Receive, especially if you have quite a list of employees to send paystub emails to.
Hope this helps . . . good luck!