We get a lot more information from phone calls than we get from the LORs.
Our original number one pick (in contrast to what I previously posted) got bumped off the top 10 after we talked to people in their program. When we hear "this one is a hard worker but not a superstar," it's a deathnell, especially given the nature of candidates we interview. When we hear things like, "This is only one of two medical students whose name I remembered in 30 years," or "The best hands and best student we had this year," it can really make a difference in the ranking.
Then we consider who wrote the letter. If we interview two people from the same program who got pretty much the same LOR, we ask the LOR writer to help us differentiate. When I see an outstanding LOR from a particular person who shall remain unnamed, I immediately get suspicious because he only writes that kind of letter if the person can kiss up really well.
So yes, the phone calls do make a difference.
--M