This is the strangest thing. I have no idea why it's happened. I did this experiment on a lark, since I was going to be melting butter and chocolate anyway. I didn't really think they would produce different results.
Below: same recipe, prepared in same way. On the left, cookies made from chocolate and butter that was melted in a saucepan. On the right, cookies made from chocolate and butter that was melted in a microwave. (In both methods, the butter and chocolate were cut up before being heated, and stirred periodically to prevent them from clumping up.)
The saucepan cookies are obviously much tighter and puffier. The microwave cookies spread much more. It's possible that I let the microwave run too long, thus burning the chocolate slightly. I'll have to test this again in the future.
Since this cookie was supposed to be puffy, obviously the saucepan melting method is preferablem, and though the microwave cookie looks better, it is dry and not as delicious.
The dough was obviously different too: (again, saucepan-melted is on left)
Baffling. Why has this happened?