Hi JustJoeyHere,
As far as I know, this is a known issue in Excel. Based on your description, you suppose add-in might cause this issue but you cant delete or disable this add-in.
Please read this Official blog which explain this issue:
http://blogs.technet.com/b/the_microsoft_excel_support_team_blog/archive/2012/04/26/hidden-dialogs-cause-excel-2010-to-appear-to-hang.aspx
In this blog the workaround is to check which add-in cause this issue then contact the
Developer of the add-in for any updates or solutions they may have. I think you can try to contact the Developer of the add-in.
If the Developer using Visual Designer in this add-in, and they want to solve this issue, please read this article:
http://blogs.msdn.com/b/pallavs/archive/2012/05/24/excel-is-showing-up-the-quot-save-as-quot-dialogue-in-background-when-custom-add-in-is-enabled-in-outlook-2010.aspx
If this work around doesnt apply to you, you can try is NOT maximize the Excel windows and to Cascade them. But this method might not work for all users, you can try it.
One more method you can try is to change a registry setting that helps with window focus:
HKEY_CURRENT_USER\Control Panel\Desktop\ForegroundLockTimeOut
Change the value to 0 and log off/log in to activate it.
There is a similar issue as reference:
https://social.technet.microsoft.com/Forums/office/en-us/b4d4c0fb-1742-45fd-ace8-c6cee1d269c4/excel-2010-dialog-boxes-hidden-behind-application-causing-application-freezing?forum=excel
Try these methods and let me know if they work for you. Im glad to help you.
Regards,
George Zhao
TechNet Community Support