Lens flare is the light scattered in lens systems through generally unwanted image formation mechanisms, such as internal reflection and scattering from material inhomogeneities in the lens.
What others are referring to as "reflection" is still lens flare, at least as I know it. It's a reflection between internal elements of the lens. From my experience, a reflection caused by a lens filter is in the same form as the light that caused it, as a filter is a flat plane. The compound curves inside the lens are what cause flare artifacts to be inverted, as is seen here.
A lens hood only helps peripheral/diffractive lens flare, as when a bright light is at or just outside the edge of the frame and diffracts into the image, generally causing a haziness and loss of sharpness.
I don't see what shutter speed or ISO would do in this case, and I've never seen a "s" mode on a Canon
mode dial
In any case, there's not a whole lot you can do in this situation, other than a more expensive lens with better coatings, or changing the angle/framing of the shot to change the light angles.