I think that many schools take the undergraduate programs and schools into consideration when they are looking at GPAs. There is a professor here at San Diego State (SDSU) who sits on the application committee that was in an Engineering major before she switched. She is definitely one that understands that some classes are more difficult than others and can affect the GPA. Taking someone like her into consideration, many graduate committees are compiled of professionals from various backgrounds and think it is important to look beyond the grades. Unfortunately there are some programs that set a cut-off GPA to limit the applications they have to review. Most of the cut-offs are pretty reasonable though. Like, SDSU's is 3.2. It used to be 3.0.
It is interesting that you say, "Like if, in the past, students from that undergrad program were admitted and looked great on paper, but didn't fare well in the grad program, the grad admissions committee may remember that next time they see an applicant from that school." I have talked to some professors here because I was concerned about not have perfect scores (average GRE) and minimal field experience but they were reassuring. They said that many programs are realizing that they have to start looking past the GPA and GRE scores. The scores are more as a brief idea of how focused the student was in undergrad. That is why many of the programs are moving towards personal interviews. They interviews give the committees an idea of how the student interact and if they are capable of keeping their cool and fluid in conversation. I wish the programs that I am applying to would do interviews. At least, they would get to meet me and interact with me.
See my response above.