this still happens just randomly for me,( 10.6.3) when I open up LP. its so annoying. not like I ever selected to hide main window.
there should be at least something that says 'your main window is hidden, click here to show'
The behavior is not random, it occurs when you try to close the session by closing the main window, but before you save your project. Because another, usually smaller window is also open, closing the main window doesn't close the project and leaves that small window open. At that point you close the small window, which means you'll close your project, so you get prompted to save your project before you save it. If you save it with only the small window open, then that's how it will open when you reopen the project later.
To avoid this behavior, when you're done working in a project, make sure you have the desired windows opened (most likely the main window at least). Now SAVE your project. Only after you've saved, close your project (File > Close Project or Option-Command-W) which will close all open windows in one operation without triggering a prompt. Your project will reopen exactly how you saved it.