These two systems cannot work together. The DOS Compatibility Card changes the characteristics of the video signal when displaying a MS-DOS/Windows screen image. These changes may vary based on the monitor that is attached, and the settings in the PC Setup control panel.
The Apple Presentation System is not be able to handle the differences in the video signal. The Apple Presentation System expects a 640x480 67-Hz Macintosh signal, but it is receiving a 640x480 60-Hz VGA signal when using MS-DOS or Windows.