Is this really the case?
* The current DC is not in the domain controller's OU
They do need to be, otherwise the Default Domain Controllers policy doesn't apply. You could like the policy elsewhere, but that's another of those that gets a big "we don't support that" flag from MS.
I'd fix that first since the policy controls access to the directory.
Any kind of replication errors are likely to be the cause of the problems with Exchange seeing the ACL changes. At least that's my theory.
Chris