We ran into a couple issues with the upgrade also regarding the AD awareness. One resolved, one still ongoing with a TAC. We do not use ISE, so I cannot comment, but the issues may at least have some similarities to give some thoughts on the issue.
Resolved: Users not being authenticated at all. The issue we found here, is that in realms the domain was listed as the FQDN (contoso.com), but because the user agent reads event logs, it reads the NT-4 type domain name (CON-COM). It has the be the exact same one for it to work.
Unresolved: Security groups that are assigned in rules are read properly by the Defense Center, but the groups are not passed through to the sensor. Some groups are, others are not, and it changes constantly. Workaround is to assign users manually to the rule, which is a massive headache.