Thank you for your quick reply. I had saved my previous projects in the same way you had suggested, and I had encountered this problem.
Hence to double check I again created 2 projects in the same manner with option box(save nvrams) checked.
First project with project name test1 with a ASA and set the int e0/0 to ip 126.96.36.199 and named it test1.Write ASA and Saved project and closed. Crosschecked startup config, Settings were saved.
Opened a new project with name test2 with a ASA and set the int e0/0 to ip 188.8.131.52 and named it test2. Write ASA and Saved project and closed. Crosschecked startup config, Settings were saved.
Now I opened the first project and when I check the ASA running config, I find the int e0/0 now has name test2 and ip set to 184.108.40.206.
Both the Config and Working folders in the both the projects are empty.
Well, you are using the same working environment for both projects (default work dir for qemu) :D
Because you didn't check the option "Save nvrams and virtual hard drives" when you created the project.