I have this problem with both Reader X and XI. My OS is Windows 7. I originally had Adobe Reader X but I uninstalled and installed Reader XI, which did not fix this behavior.
This problem occurs when I open PDFs for the first time. The title bar appears above the top of the screen, out of reach. It happens whether I first save the file and open it, or open directly from the browser. If I resize the Reader window in any way (using the edge of the window), the title bar snaps down to where it should be, but it I resize horizontal (the window width) the window moves down and the bottom edge goes out of reach. If I reopen a PDF, it saves the previous window size because of the setting in Preferences.
This is very annoying because I can't close/minimize PDFs without resizing them first, and I open many PDFs per day.
Thank you for your help.