Being off by one in your ortho projection...

has strange effects.  See

https://github.com/rswinkle/opengl_reference/blob/master/src/multidraw2.cpp

Only the right/upper half of the squares move, but the interpolation
within the squares is affected, though less and less as you get closer
to the screen space origin (ie lower left).

demos/multidraw.cpp

@@ -35,6 +35,8 @@ typedef struct My_Uniforms
 
 int polygon_mode;
 int use_elements;
+int minus_1;
+matrix_stack mat_stack;
 My_Uniforms the_uniforms;
 
 void cleanup();
@@ -108,9 +110,7 @@ int main(int argc, char** argv)
 	glUseProgram(program);
 	pglSetUniform(&the_uniforms);
 
-	matrix_stack mat_stack;
-	//rsw::make_perspective_matrix(mat_stack.stack[mat_stack.top], DEG_TO_RAD(45), WIDTH/(float)HEIGHT, 0.1f, 100.0f);
-	rsw::make_orthographic_matrix(mat_stack.stack[mat_stack.top], 0, WIDTH-1, 0, HEIGHT-1, 1, -1);
+	rsw::make_orthographic_matrix(mat_stack.stack[mat_stack.top], 0, WIDTH, 0, HEIGHT, 1, -1);
 
 
 	unsigned int old_time = 0, new_time=0, counter = 0;
@@ -237,7 +237,17 @@ int handle_events()
 				} else {
 					puts("Using MultiDrawArrays");
 				}
+			} else if (sc == SDL_SCANCODE_M) {
+				minus_1 = !minus_1;
+				if (minus_1) {
+					puts("minus_1");
+					rsw::make_orthographic_matrix(mat_stack.stack[mat_stack.top], 0, WIDTH-1, 0, HEIGHT-1, 1, -1);
+				} else {
+					puts("all the pixels");
+					rsw::make_orthographic_matrix(mat_stack.stack[mat_stack.top], 0, WIDTH, 0, HEIGHT, 1, -1);
+				}
 			}
+
 		}
 	}
 	return 0;

testing/multidraw.cpp

@@ -80,6 +80,7 @@ void test_multidraw(int argc, char** argv, void* data)
 	pgl_uniforms the_uniforms;
 	pglSetUniform(&the_uniforms);
 
+	// TODO This shouldn't be WIDTH-1, HEIGHT-1, will have to update expected output
 	make_orthographic_matrix(the_uniforms.mvp_mat, 0, WIDTH-1, 0, HEIGHT-1, 1, -1);
 
 	glClear(GL_COLOR_BUFFER_BIT);