On a smaller CNC machine you are probably going to be happier with smaller cutters at higher RPM and feed rate. The exception being face mills that are cutting wide, but shallow. I tend to stick with 1/4-3/8" cutters. They have the advantage that they are cheaper too.
On a manual machine there tends to be the desire to pick the largest cutter you can find, and bury it as deep as possible. CNC is a different creature, and you don't necessarily want to follow the same path.
Another thing occurred to me this morning, how are you entering the material? Plunge, or helical ramp? If you are plunging, that is pretty rough on cutters. A helical ramp will let you engage more smoothly, and put a more constant load on the cutter.