Ok someone tell me where my vote goes. I currently ride a bike that Salsa calls a 56cm frame. It has a 56 cm ctc TT, a 56cm ctc ST which is 58cm ctt (other brands would measure it that way). I am about to buy a Specialized that is called a 54. It has a 54.8cm ctc TT (eff), and a 45cm ctc ST which is 50cm ctt.
Personally I look first at effective TT so I will call the first bike a 56 and the second a 55.