Hi KyleCarlson,
Based on your description, my understanding is that you opened an Excel file and then try to open a new Excel file. But the new Excel file was opened behind existing Excel window.
Is my understanding correct? Please tell me if this issue only occurred in Office programs? Which version of Windows are you using?
Ideally, Windows System default to set new windows in the foreground. Have you every checked the Add-ins in Office programs and the third-party in Windows System.
I suggest you perform a clean boot in Windows to troubleshoot, about how to perform a clean boot please refer to this link:
https://support.microsoft.com/en-us/kb/929135
Please try this method and check if it works for you, if your issue still exists please provide more information.
I'm glad to help and follow up your reply.
Regards,
Emi Zhang
TechNet Community Su