フルスクリーンとウィンドウモードを切り替えられるプログラムと、
3D描画を合わせてみたところ、フルスクリーンとウィンドウ時で描画結果が変わってしまいました。
自分では原因の見当がつきませんでした。
良ければご指導お願いします。

#include "DxLib.h"
#define SCREEN_SIZE_X 640
#define SCREEN_SIZE_Y 480

int WINAPI WinMain(HINSTANCE hInstance, HINSTANCE hPrevInstance, LPSTR lpCmdLine, int nCmdShow)
{
	int SubScreen;
	int WindowFullSize;
	int WindowPosX;
	int WindowPosY;
	int DesktopSizeX;
	int DesktopSizeY;
	int ff = 0;

	ChangeWindowMode(TRUE);
	GetDefaultState(&DesktopSizeX, &DesktopSizeY, NULL);
	SetWindowSizeChangeEnableFlag(FALSE, FALSE);
	SetGraphMode(DesktopSizeX, DesktopSizeY, 16);
	SetWindowSize(SCREEN_SIZE_X, SCREEN_SIZE_Y);
	SetWindowStyleMode(5);
	if (DxLib_Init() < 0) return -1;
	SubScreen = MakeScreen(SCREEN_SIZE_X, SCREEN_SIZE_Y);
	WindowFullSize = FALSE;
	SetUseZBuffer3D(TRUE);
	SetWriteZBuffer3D(TRUE);
	while (ProcessMessage() == 0 && CheckHitKey(KEY_INPUT_ESCAPE) == 0)
	{
		ff = (CheckHitKey(KEY_INPUT_F4) ? ff + 1 : 0);
		if (ff == 1)
		{
			if (WindowFullSize)
			{
				WindowFullSize = FALSE;
				SetWindowStyleMode(5);
				SetWindowSize(SCREEN_SIZE_X, SCREEN_SIZE_Y);
				SetWindowPosition(WindowPosX, WindowPosY);
			}
			else
			{
				WindowFullSize = TRUE;
				GetWindowPosition(&WindowPosX, &WindowPosY);
				SetWindowStyleMode(2);
				SetWindowSize(DesktopSizeX, DesktopSizeY);
				SetWindowPosition(0, 0);
			}
		}
		if (WindowFullSize)
			SetDrawScreen(SubScreen);
		else
			SetDrawScreen(DX_SCREEN_BACK);
		ClearDrawScreen();
		SetCameraScreenCenter(SCREEN_SIZE_X / 2, SCREEN_SIZE_Y / 2);
		DrawBox(0, 0, SCREEN_SIZE_X, SCREEN_SIZE_Y, GetColor(255, 255, 0), FALSE);
		SetCameraPositionAndTarget_UpVecY(VGet(-200, 200, -200), VGet(0, 0, 0));
		DrawSphere3D(VGet(0, 0, 0), 50, 8, GetColor(255, 0, 0), GetColor(255, 255, 255), FALSE);
		DrawLine(SCREEN_SIZE_X / 2, 0, SCREEN_SIZE_X / 2, 153, GetColor(255, 255, 0), FALSE);

		if (WindowFullSize)
		{
			int DrawSizeX;
			int DrawSizeY;
			SetDrawScreen(DX_SCREEN_BACK);
			ClearDrawScreen();
			if ((float)SCREEN_SIZE_X / SCREEN_SIZE_Y < (float)DesktopSizeX / DesktopSizeY)
			{
				DrawSizeX = DesktopSizeY * SCREEN_SIZE_X / SCREEN_SIZE_Y;
				DrawSizeY = DesktopSizeY;
			}
			else
			{
				DrawSizeX = DesktopSizeX;
				DrawSizeY = DesktopSizeX * SCREEN_SIZE_Y / SCREEN_SIZE_X;
			}
			DrawExtendGraph(
				(DesktopSizeX - DrawSizeX) / 2,
				(DesktopSizeY - DrawSizeY) / 2,
				DesktopSizeX - (DesktopSizeX - DrawSizeX) / 2,
				DesktopSizeY - (DesktopSizeY - DrawSizeY) / 2,
				SubScreen,
				FALSE
			);
		}
		ScreenFlip();
	}
	DxLib_End();
	return 0;
}