First, upgrade to at least App Layering 4.10. The following registry key is only functional in 4.10 and later. This behavior will be enabled by default in 4.12, so once 4.12 is out, ignore this article and just get upgraded.
Add a version to each of your platform layers that you intend to use with multi-NIC Target Machines, or create new Platform Layers. In that new platform layer version, add the following registry value:
KeepConfigValue is a DWORD that must be set to 1. It changes how we capture and process network information in multi-NIC environments.