You're de-emulsifying the dough. You worked so hard to combine all those ingredients, and under the pressure of the vacuum, you're pulling them apart, at least to some degree.
If you're intent on specifically vacuum-packing the dough, then I'd follow Chefross's advice and freeze it first.
I personally make logs out of all my cookies doughs, shaping and wrapping with 24" wide plastic wrap, and freeze. I use a Forschner 10.25" Bread Knife and cut through while frozen and bake. While they go into the oven looking more like very uneven cubes, they come out surprisingly round and similarly shaped. Works when selling smaller cookies by the pound, or not selling them period :-)