The reason for the different values is the following:
During oxidative phosphorylation, each reduced NAD molecule has the potential to produce 3 ATP molecules, and reduced FAD has the potential to produce 2 ATP. However, 25% of the energy produced from the electron transport chain goes into actively transporting ADP into the mitochondria (how else would they make ATP? ADP+Pi-->ATP). Thus, the total number of ATP molecules they *actually* produce is 75% of the two values: namely, 2.5 ATP for reduced NAD, and 1.5 ATP for reduced FAD.
I hope that clarifies it