At the time of setting up the Microsoft 365 subscription, when the Exclaimer Cloud IP addresses are added to the whitelist - a prompt is displayed that tells you to run the Enable-OrganizationCustomization command.
This issue occurs because certain objects are consolidated in most of the Microsoft datacentres to save space. And, when you use the Exchange Online PowerShell (or the Exchange Admin Center) to modify one of these objects for the first time, you get the prompt to run the Enable-OrganizationCustomization command.
For more information, see the Microsoft TechNet article.
Exclaimer Cloud will automatically run the necessary commands for you; however, it may take up to one hour to take effect.
After some time has passed, try to re-run the Microsoft 365 connector setup.