RE: bow riser blocking site window...normal?
 

Rick,
I had the same problem on my PSE when I bought it a few years ago. I didn't know much, just starting out in archery(nothing has changed!) and took it to a different pro shop. Turns out the aim cables were positioned on the wrong side of the cable guard guide. That's all it took. Take a photo of the bow, showing the setup,and post it. I bet someone here will have the answer for you.
Good luck.

RE: bow riser blocking site window...normal?
 

I think it may have something to do with your hand placement putting on a little torque. I agree post some pics. When you are looking at the target, how much of the pins stick out from behind the riser?