I am learning to use the allegro library right now and when using the set_gfx_mode function if I use GFX_AUTODETECT_FULLSCREEN for the first argument the window will go fullscreen when running the compiled application, but after about the first second of running, all the colors change. Using any other graphics mode this doesn't happen, but on two separate machines the colors change just after changing to fullscreen mode. Has anybody else seen this happen before? I can't find any discussion on this problem at all.
I am using the pre-compiled allegro 4.4.2 library for visual studio 2010 and running windows 7.
Allegro 4 is old and uses APIs that are no longer very well supported by modern operating systems. The full screen mode is going to be buggy, especially on 8-bit graphics. The best way to get a reliable full screen is to honor the user's current desktop settings:
int w, h;
get_desktop_resolution(&w, &h);
set_color_depth(desktop_color_depth());
set_gfx_mode(GFX_AUTODETECT_FULLSCREEN, w, h, 0, 0);
Then your application will need to center/scale the drawing. It's not really that difficult, just draw everything to an intermediate buffer that is the width/height of your native game, and then stretch blit it to the appropriate screen size.
All that said, you should really be learning Allegro 5 as it is designed to work on today's hardware and operating systems, including iOS and Android.