My guess is that the package still references config2.

This is the order in which configs are applied:

1. Apply package configurations. (--> conf2)

2. Apply configurations specified in jobstep (--> conf3)

3. Re-apply package configurations (--> conf2)

So basically conf2 is overwriting conf3.

I would edit the package in your development machine, remove the package configurations, redeploy the package and specify the config file in your jobstep.