The behaviour should not be dependent on the OS.

What is this "SSIS new project for flat file conversion "?

There are only two ways of developing SSIS projects:

* Project Deployment Model: this one is new and is introduced in SQL Server 2012. The question deals with this Model only.

* Legacy Deployment Model: this one corresponds with earlier versions of SSIS (2005 - 2008R2).

It is possible that you had your project first in Legacy Deployment Model, as that Model did copy the .dtsx packages into the bin folder. However, the Project Deployment Model creates an .ispac file and puts the .dtsx inside it.