What SSIS is doing is the following (if I read it correctly, because it is such a mess):

1. Load configurations specified in the package configuration window during design time.

2. Check the command line. With the command line, you can for example alter a connection string pointing to a configuration specified in step 1, effectively altering the configuration.

3. Reloading the configurations of step 1. If step 2 altered something, it will load thus new configurations.

However, if you specify a brand new config file in step 2, it will be overwritten by the design time configurations in step 3.

Why don't the other package fail? I dunno. Bad SSIS mojo. 🙂