So I am having an issue that is driving me crazy. We sync all of on-prem AD to Azure and we are not filtering out any OUs or anything like that. Only about a third of all on-prem groups show in Azure, this includes mail enabled, distribution and security. So why are 2/3 of our groups not in Azure? I have created multiple test groups of different types in different OUs, I have compared the attributes of groups I see in Azure with those I don't and there are no glaring issues. I have manually run Azure AD Connect to sync with Azure. There are no sync errors, I see the test groups I create being picked up in the Delta Import. I have run IdFix and none of the missing groups are listed.
So for the life of me I cannot figure out why it appears that all the groups are syncing but only 1/3 of them show up in Azure. We have both Azure AD Connect and Azure AD Cloud Sync running. We are only seeing 1046 out of 3018 groups.
Any help would be greatly appreciated.