Given that you state M & S modes, I don't think it's slow sync that's the problem - you choose the shutter speed in those modes, and if you want a slow shutter, you set it and that's what you get. You can't set Slow sync (though you can set rear sync) in M or S. Also, I'd observe that in Manual, you choose the exposure settings, not the camera, unless you have Auto ISO enabled.
Probably what you're seeing is that the built-in speedlight is used in TTL-BL mode when using Matrix or CW metering. That makes it work in a sort-of Fill Flash mode. With spot metering, the flash works in straight TTL mode and will try to illuminate the subject on its own.