Having just upgraded from 1019 to 1063 I find that all my Delphi 2007 builds acquire the "Generate Console Application" checkbox and get built as console applications. Very luckily I spotted that a console window was opening behind every application that I ran, just as we were working towards a major new release of our product.
The Linker page is disabled ('settings will be loaded from the project file') and when the FB project is opened, the Console checkbox is clear (except on the few build actions that are really console apps). The projects build correctly in the IDE, and the project file does not have the console flag set, but as soon as the action has run in FB, the (still greyed) Console checkbox is becomes checked and the built application opens a console window when run. Even DLL builds acquire the Console checkmark, though this seems to be benign.
The greyed Console checkbox persists if the FB project is saved and reloaded, but dropping back to build 1019 resolves the problem and also clears the greyed checkbox as soon as the action runs.