Jeff:
My initial thoughts looking at your mold pictures and considering the initial tool your using and the machine I am not too surprised you would be having trouble. The first problem your having is that the spindle really can't run any where fast enough on the Pocket NC for that type of work with such a small cutter. SFPM on 6061 is like 1000-1500 SFPM
The formula for RPM is
SFPM * 4 / CUTTER DIA =
1000 * 4 / 0.03125 = 128,000 RPM yet the Pocket NC only runs at 10,000
This doesn't mean you can cut. It just means you really have to do some compensation.
First your feed rate must be decreased. And you chip load must also decrease from a normal calculation.
Second your relieved part of your tool should be no more than what will cut your part.
If your cavity is only 1/8" deep then the total tool tip should be just a little more than that.
What I see from the initial cutter is 1/32 diameter that is probably 3/8" long. that is before you hit the 1/8" diameter shank. It's just too fragile for any real cutting.
So find the shortest tool to do the job, run the spindle at max rpm, and do super light depths of cuts like maybe 0.001"-0.003" (Axial depth of cut) and very light step overs like 0.003" (Radial step over)
Well that's my initial thoughts.