Software Deployment

This is a new one on me. I have a new software package that looks like it was developed well. It came as 2 CD's but 4 different packages. 3 of the 4 packages install as an MSI. The last is a setup.exe that then launches an MSI file that temporarily places it in the temp folder. Once the MSI launches it then runs InstallShield, and has prompts, one being important to us. The prompt has checkboxes with all the states listed, we need NC data. The problem we have is this package goes from Setup.exe to MSI to InstallShield Wizard so I can't run the record feature on the setup.exe. When we extract the MSI it runs and all we've done is skip the setup.exe step but InstallShield wizard still comes up. We need the ability to tell the package to select NC checkbox but can't because of the MSI. This is a very strange package, I've never seen it wrapped up like that. Does anyone have any ideas?

Thanks.