What went wrong with these pots de creme au chocolat? I baked pots de creme au chocolat yesterday following this recipe, but something went wrong:

As you can see in the photos below, the chocolate seems to have separated out, forming a relatively firm top layer, while the remainder underneath is lighter in color and has an unappetizing wet mousse-like texture.



I followed the recipe closely, but let me add some clarifications to avoid ambiguity:


I made the chocolate variant only, so doubled the quantities of dark chocolate (I used 65%) and cocoa
I beat the eggs and sugar in a stand mixer with a wire whisk attachment, then added the infused milk and then the melted chocolate while still mixing on low speed
I poured the resulting mixture into eight 4oz glass canning jars (~3oz per jar). At this point, the mixture appeared to be homogenous.
I arranged the jars in a 9x12x2" steel pan, placed it into an electric oven preheated to 320 degF, then filled the pan with boiling water to about halfway up the glass jars. 
I baked these until the tops would hardly wobble when I tapped the jars, which was at the 29 min mark
Once I removed the jars from the water bath, the layering was immediately obvious in all eight pots de creme. Interestingly, the bottom of the chocolate layer seems to roughly align with the water level in the bath.
After cooling briefly, I put lids on the jars and refrigerated them for several hours. The photos above are after refrigeration overnight.


The only possibility I can come up with is that I inadvertently filled the pan with cold water. I used an electric kettle, and while I thought I heard it bubbling in the background, my attention was focused on another recipe. Maybe I never switched it on.

Is this a likely explanation for these results? I can see how a cold water bath would result in uneven cooking, but I haven't been able to find good reasoning for why the chocolate would separate out on top.
You've answered your own question. The water bath should have gone all the way up to just above the crème in your pots. I'd also bet that you had this on the top rack of your oven, this type of water bath should be on the lowest rack to keep the tops from cooking faster than the bottoms which is what looks like happened. I've had the same thing happen with crème brulee before.


  Once I removed the jars from the water bath, the layering was
  immediately obvious in all eight pots de creme. Interestingly, the
  bottom of the chocolate layer seems to roughly align with the water
  level in the bath.