Nick,
I've never grown Cornelian cherry but here's some info from Bernheim Arboretum and Research ( http://www.bernheim.org/cornus_mas.html ) that might be helpful. Sounds to me like you're doing everything right.

"Cornelian cherry dogwood can be propagated by seed and softwood cuttings. Seed require a warm moist stratification for up to 120 followed by 90 to 120 days of cold. Softwood cuttings can be taken in June and July."

Art

I winter sowed both kousa dogwood and regular white-flowering dogwood (Cornus florida) two years ago and got 100% germination from the seeds. Trees grew about 14 inches per year. Last year I winter sowed apple & pear tree seeds and again had 100% germinate. This year I've sowed Acer palmatum/Japanese red maple, Cornus sericea/red-twig dogwood & apple. Germination should occur sometime around the middle of April based on last year's results.

Winter sowing is a USDA-approved method of growing annuals, perennials, vegetables, trees, shrubs, etc. in recycled containers set outside in winter. There is a winter sowing forum here on GardenWeb.

I have sown white-flowering dogwood (Cornus florida) directly into the ground and lost all to chipmunks and squirrels (rats with bushy tails). The few that sprouted were eaten immediately after sprouting in the spring.

This year I have winter sown into milk jugs and hope for better results. See Winter Sowing Forum:
http://forums2.gardenweb.com/forums/wtrsow/
and the winter sowing FAQ:
http://faq.gardenweb.com/faq/wtrsow/

I previously stratified, but the instructions I read said nothing about warm stratification. I pulled off all of the pulp from the berries and soaked the seed in warm water for about 4 hours. Mix some warm water with some sifted sphagnum peat. (Shaking the peat and water in a jar is a quick way to moisten the peat. All excess moisture should be squeezed out of the peat. Too much water will rot the seed.) Mix the seed with the damp peat. I put the seed/peat mixture in a zip lock bag. (Punch a few air holes in the bag.) Place bag in refrigerator for 100 days. Check occasionally to be sure the peat is still moist.

A few of the seeds were already sprouting after 100 days. I planted the seeds/seedlings in an outside transplanting area. The squirrels and chipmunks soon ate those, also.

I may try to winter sow these directly into the ground, and put a quarter-inch-hardware-mesh wire cage over the top. (Something similar to a bottomless bird cage.) A few bricks on top to keep the critters from pushing/pulling it off will hopefully aid in survival of the seedlings.

Here is a link that might be useful: http://faq.gardenweb.com/faq/wtrsow/