Run times are important, but at the academy they are not weighted as highly. The AFT (1.5mi) makes up 15% of your PE Average. The PFT run (600m) makes up 1/5th of your PFT score. The PFT counts as 50% of your PEA...and your PEA does not make up a huge percentage of your Overal Performance Average. So, running makes up 25% of your PEA and about 5% of your OPA (I don't remember what percentage of OPA is PEA related).
The AF PFT places MUCH more weight on running (the 1.5mi).
Obviously, failing things is bad! PEA is usually not the thing most cadets worry about...unless they are at/below the 2.0 line