The factory doesnt have enough output slots. Some items with more than 6 inputs, the extras are deleted (for example, your own factory t3, the modules go bye-bye)
Are you using the latest v9.0.3? I did fix this issue in v9.0.2, and testing with mostly vanilla modlist at default settings, each machine has 8 output slots for me.
Ah, so just to verify, the issue is fixed now, right? Because if it isn't for some reason, I would want to look into it; but hopefully should be fixed!