I have opened the data in InRoads 08.11.07.566 (SS2) and in 08.11.09.493 (SS3) and gone through the Roadway Visibility tools and do not see any obstruction in either version of the software. Please not that I do not have your preference file to use the same saved settings for the command, so the offsets, eye postiion, object, position, etc may not be the same for me to duplicate the obstruction.
When testing, I set the interval to 10 feet, sight distance to 180, and relaxed distance to 100. Then for the position I turned off all offsets, set the eye height to 3.5 feet and the object height to 2.0 feet. This yielded no differences between the two versions and I saw no obstructions.
Make sure all options are the exact same between the two versions by loading the same preference file and loading the exact same preference for the command in the different versions. If you still have issues, please update this forum post with the XIN for further testing.