According to Taking Advantage of High-Definition Mouse Movement, it should be by design.
The primary disadvantage to data from WM_MOUSEMOVE is that it is limited to the screen resolution. This means that if you move the mouse slightly — but not enough to cause the pointer to move to the next pixel — then no WM_MOUSEMOVE message is generated. So, using this method to read mouse movement negates the benefits of high-definition input.