Ben Franklin,
I wasn't aware that many transitional spots don't fill every year...from what I know they almost all (or maybe all) fill. The transitional years tend to be hard to get because most of them are quite a bit easier than preliminary medicine or surgery years, and also they get to rotate through more different areas. The transitional years are usually filled by folks going in to fields like radiology and ophthalmology, who tend to be in the top of their medical school classes. This makes the competition fierce. Also, there aren't as many transitional year programs as there are medicine or surgery prelim programs, so there are just less spots available.
Surgical preliminary years, on the other hand, sometimes go unfilled. This is because it's very hard work and sometimes not that much learning.