http://www.physicsclassroom.com/Class/refrn/u14l1e5.gif
http://farm5.static.flickr.com/4087/5079912762_85e23ba4c6.jpg
If there is any angle on the laser when it comes in to glass, lexan, or acrylic there will be some refraction. I honestly couldn't say if there is zero angle. Perhaps it will go right through, but very rarely will a sniper have a straight horizontal shot. The images above show what happen with an angle.
The thicker the material, the more refraction there will be. All light is refracted with these materials at angles. The deviance may not be noticeable with thin windows, but it does exist. In a real world example it may or may not be enough to ruin the shot, but it should be considered. Since transparisteel is a fictional material, I assume it has properties similar to acrylic but that would be up to the Game Master.
I hope this helps. If not, that is all I am going to provide for you on this topic of physics.
More importantly for a game perspective is the intention of the designer of the window. If the window is designed to protect a VIP, as in the example given, I would assume that the designer would take into account all common weapon forms that may be applied.