Yes you do need clearance over the top tube, 2 inches is good. The thing is about a LBS is sometimes you get what you experienced. I am going to include some sites for you to look at about fit.
http://www.aboutbikes.com/abweb/bike%20fit.html
http://www.bontrager.com/rants/myth_of_kops.html
http://www.rei.com/EGA/clinics/bikefit2f.html
This should clear up any questions you may have. Hope this helps.