Hi Andrey,
It looks like there are a couple things going wrong here. In the attached PDF the rectangles have zero width and a transparent stroke color. The XOD conversion is not specifying the annotation width in the XFDF so WebViewer uses the default value of 1. We'll investigate and resolve this issue in the conversion.
Since the color is not specified in the XFDF, WebViewer should display it as transparent, however it's incorrectly setting the default color value to black. We'll fix this on the WebViewer side so that it's handled correctly.
What you could do for now is update the annotation deserializing code so that if color isn't specified it will be set to transparent. This is the change we'll be making inside WebViewer for future versions. You can add the following to your config file:
var deserialize = Annotations.Annotation.prototype.deserialize;
Annotations.Annotation.prototype.deserialize = function(element) {
deserialize.apply(this, arguments);
if (element.getAttribute('color') === null) {
this.StrokeColor = new Annotations.Color(0, 0, 0, 0);
}
};