RESOLUTION
To resolve this problem you should add the permissions to be inherited to the C2RegACL.inf file.
Example:
Section of C2RegACL.inf before modifications:
[HKEY_LOCAL_MACHINE\SOFTWARE]
BUILTIN\Administrators = FULL
CREATOR OWNER = FULL
SYSTEM = FULL
Everyone = QV, SV, CS, ES, NT, DE, RC
Section of C2RegACL.inf after adding inherited permissions:
[HKEY_LOCAL_MACHINE\SOFTWARE]
BUILTIN\Administrators = FULL
BUILTIN\Administrators = INHERIT, FULL
CREATOR OWNER = FULL
CREATOR OWNER = INHERIT, FULL
SYSTEM = FULL
SYSTEM = INHERIT, FULL
Everyone = QV, SV, CS, ES, NT, DE, RC
Everyone = INHERIT, QV, SV, CS, ES, NT, DE, RC
Note the INHERIT entry in the permissions. This is the option that sets the permissions that will be inherited by subkeys.