Shankara,
I think there is something wrong with either your workspace or your project… I have tried every possible variation of your directory structure and cannot reproduce this problem at all… can you try and create a new Workspace, and a new project and slowly create files until it breaks… when it DOES break, export that projec tto a ZIP file and sent it to support@genuitec.com so we can see what you are doing and if we have a bug or not.
Thanks!