Use the exclude registry key from processing. Attached is a Word document with screenshots showing where to set that up.
It will need an entry for each of the registry entries that got flagged in the agents log (attached). But you can use wildcard characters.
In the Exclude These Registry Keys From Processing box, enter registry keys that will not be included in the ReACL process. A leading '\' is not necessary. Separate the paths by pressing Enter. The following wild card characters are permitted when specifying registry keys:
* matches zero or more characters in a key name, but not the '\' path delimiter.
? matches any single character.
** matches zero or more parent keys.
Examples:
HKEY_LOCAL_MACHINE\SOFTWARE\XYZ – a single key
HKEY_LOCAL_MACHINE\SOFTWARE\XY* – all keys starting with "XY" in HKEY_LOCAL_MACHINE\SOFTWARE
HKEY_LOCAL_MACHINE\SOFTWARE\?YZ – all 3-character keys ending with "YZ" in HKEY_LOCAL_MACHINE\SOFTWARE
HKEY_LOCAL_MACHINE\**\XYZ – all keys named "XYZ" anywhere under HKEY_LOCAL_MACHINE
**\XYZ – all keys named "XYZ" in any registry hive