It's actually two different but related glitches with two different games.

Raptor: Call of the Shadows -- In fullscreen mode, if I skip the introductory sequences by repeatedly hitting enter without touching the mouse, and then click the left mouse button on "New Mission", the mouse cursor jumps to the corner of the screen rather than the game registering the click. When I continue from there with the mouse, it proceeds normally until I click on "Fly Mission"... then I hear the sound effect and the music, but the screen won't advance until I click the right mouse button, or hit alt-enter to leave fullscreen.

Rise of the Triad -- On the intro screen with the "Apogee" logo, if I click the left mouse button without moving the mouse, the music still plays but everything else freezes until I click the right mouse button or hit alt-enter to leave fullscreen.

Can anyone else reproduce these glitches? Of course it is easy to get around this, but I am still curious why they are happening and how I can fix it. I am running DOSBOX on Windows Vista Home Premium with Intell integrated graphics, and I have a Logitech cordless mouse. I've tried different mouse settings, graphics output settings, etc. to no avail.