I'm on Linux Mint, version 2.1. When I click on the menu File > Save, or hit Ctrl+S, on an existing project, it opens the file explorer so that I can select the path to save, in other words, it works the same as the "Save As" command. It's kind of annoying because it also doesn't memorize the directory from which I opened the model, so I have to navigate all the way to the original path.
Also, maybe related, whenever I click to close the app, it asks me if I want to save changes, even if I have just saved, or didn't change anything at all.