It depends on the program or at least that's what I found in Texas.
I had a crappy GPA as an undergrad (2.79 overall & maybe a 2.4 science), but I'm doing great in my master's program at Texas State (3.59 see I'm not stupid). However the only program that was willing to look at my master's work was UT. All the other programs told me I would have to retake some class but I know that some schools also average (UT does). So what's the point in taking the class over again if the school is going to average the grades? You would have to take the class 3 times to get an A average. I also teach organic chemistry labs so why am I going to retake a class that I currently teach?
Anyway, UT did tell me that my application would have to be looked at personally because the initial ranking that they would give me would be based on my undergrad GPA. Obviously they did look at my application personally because I just interviewed with them last week.
My biggest suggestion is to find the program that you want to go to and ask admissions what you have to do in order to get in.