MSI Install always installing all features when run in silent mode

I have a large MSI based install that installs three different versions of our program. The SN entered by the user decides what version of the program gets installed and selects features based on that. This all works great when run normally with the UI but when we run it with a /qn swithc to run it silently it always installs all features and I cannot figure out how to selectively turn some features off. I do have installscript functions that are called with custom actions and those are working except the feature selection. I have tried from the commandline too but it always installs everything.

How can I turn something off?

Brandon Lowe