I haven't tried to replicate your situation. But personally I use this c# code in my game:

if (Input.GetButtonDown("Fire1"))
{
    Ray ray = Camera.main.ScreenPointToRay(Input.mousePosition);

    RaycastHit hit;
    if (Physics.Raycast(ray, out hit, 100))
    {
        //....
    }
}

And it's been working on PC/Mac/Web/Android and iOS in all resolutions, for button clicks and touches on the screen.

You probably want this in some singleton class called "Input" or something so you don't call it for every object in the game. Call it from some main object and then call some method on the object you clicked on.

I'm having this exact same issue. My colliders work all day in Free Aspect. The minute I make a build at 1024x768, they stop working however. I've used the same methodology/code to handle OnMouseDown events for years now. Short of writing my own raycasting, did you ever find a workaround?,I'm having this exact same issue with some colliders in my scene. They work fine in free aspect, but not in standalone.