If, after calling SDL_SetVideoMode() to resize the window, SDL receives a ConfigureNotify event for the old size, SDL_PrivateResize() will be called with the old size, generating an SDL_VIDEORESIZE event and (significantly) calling SDL_SetMouseRange() on the given size.  When the ConfigureNotify for the resized window comes in, it will be dropped because it's the same as the current window size, meaning that SDL_SetMouseRange() still has the old size; if that is smaller than the actual window size, then SDL_GetMouseState() will only return coordinates within that smaller size.

For example, when resizing a window from 800x600 to 1024x768, if a ConfigureNotify for 800x600 comes in after SDL_SetVideoMode(1024,768,...), then SDL_GetMouseState() will only return mouse coordinates in the range (0,0)-(799,599).

I haven't succeeded in reproducing the issue in a simple test program; it may be a race condition that only manifests under load or with a particular code sequence.

The fix is probably to ignore all ConfigureNotify events after a window resize until one is received for the new window size.