Modifying Sylink before installation

I have wrote a tool to modify domainID and preferredGroup in the Sylink file, before running the msi file. Sylink is changed, and SEP client is installed in the correct domainID, but the group stays always in the default group. I can't find why this is happening. Checking the registry keys for Sylink, current group is defualt group and preferred group is the group I configured.

Any idea how to get around this?!