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The recipe called for simply melting bittersweet chocolate with about a tablespoon of vegetable oil. The chocolate coating was too thick and didn't harden effectively until I put it in the fridge for a bit. Then it wasn't very stable or attractive when the cookies sat at room temperature for a couple of days.
I do not like to use chocolate chips for dipping candies or cookies for just the reason you mentioned. Not sure if you melted over a double boiler or microwave? most microwaves these days are too powerful to slowly melt the chocolate and actually just cook it! You will get a better result if you melt it slowly over simmering water and use a good quality chocolate product. I swear by the ghiradelli candy dipping bar (available in a 2.5 lb size at Sam's club)--glossy look, shelf stable. I have posted a picture of my maple cream buckeyes using their product, http://www.food52.com/recipes...
As lorigoldsby explains, you'll be much better off if you use a true dipping chocolate for, well, dipping. The quantity and quality of its fats are very different and suited for dipping, then setting up at room temperature.