The Admin and Wizard guides tell you how to customize deployments: www.adobe.com/go/acrobatetk.
Without knowing what your updates order is, seeing your cmd line, and having a list of what preferences have changed, it's not possible to troubleshoot your problem.
Here is some info that may help:
- Read the docs above.
- Admins usually create an MST file with the Wizard that which contains customizations.
- The update order is 9.5 > 9.5.1 > 9.5.2 > 9.5.3 > 9.5.4.
- OOC security updates do not change settings.
- There is no master switch to disable preference updates and updating with an MSI in the workflow and no MSI means that your customizations may be lost.
hth,
Ben