Hi @Glenn Maxwell,
To help you better, let me check with you first. If you want the sent emails will be saved to the user’s Sent Items folder instead of shared mailbox. You can turn off the settings that you made by replacing $true with $false in the [Set-Mailbox] command. For example, you can run the command:
Set-mailbox sharedmailbox@contoso.com -MessageCopyForSendOnBehalfEnabled $false
Set-mailbox sharedmailbox@contoso.com -MessageCopyForSentAsEnabled $false
You can refer to the documentation linked below for more information about it: Automatically save sent items in delegator's mailbox in Exchange Online | Microsoft Learn.
However, if you want the sent emails from shared mailbox should be saved to Sent Items of shared mailbox, you can first check the value by these steps:
-First, you need to connect to Exchange Online PowerShell.
-Run the following cmdlet: Get-Mailbox -Identity sharedmailbox@contoso.com | FL MessageCopyForSend*.
-If the value displayed is false, you can run the cmdlets that you mentioned above to change it to true.
Hope these could be helpful, if I have any misunderstanding or you have any other questions, please feel free to post back.