Flat chewy cookies turn out puffy and cakey. Why?

I think everyone just searches for their idea of the perfect (insert item). I always keep in mind that my idea of the ultimate is only my taste and someone else may have a totally opposite view of what is the ultimate. My tastes and recipes are always being tweaked. The only exception to that are family recipes like my mom's macaroni salad and her cloudless oatmeal cookies. To me, those are perfection.

Coke...preferably Mexican coke in a glass bottle. I have one maybe twice a year. :)

Nancy, I'm really glad that you like them. If you want to get nerdy about it, here's a great article about how different ingredients and aspects of cookie baking affect the texture and appearance:
http://sweets.seriouseats.com/2013/12/the-food-lab-the-best-chocolate-chip-cookies.html?ref=search

One was the "marvellous, magical cookies from food 52, the other was an Alton Brown Recipe. I am afraid I am a Luddite and do not know how to add things to these posts

Nancy, I, too, have made the magical cookies (my own recipe) and had them come out puffy and cakey. I suspect in that recipe that the culprit is the additional ingredients. (Some granola probably absorbs more liquid or is more acidic than others, causing the leavening to work differently.) Also, and this is entirely my fault because I used volume instead of weight as measurements, you may be packing your flour too tightly when you measure it. mrslarkin has a recipe for chubby chocolate chip cookies that she created when she accidentally added an extra cup of flour to her usual cookie dough recipe. So if there's too much flour, they may come out more puffy and chewy. Make sure you stir your flour well, scoop it lightly into the measuring cup, and level off the top. I hope this helps.

Hmm...while its not my go-to, Alton's "chewy" recipe has always produced results for me. A couple that I've tried it FANTASTIC results though are:

http://www.foodiecrush.com/2015/05/milk-bars-salted-chocolate-chip-cookies/

http://www.browneyedbaker.com/cooks-illustrated-perfect-chocolate-chip-cookies/

the latter is made with brown butter, which Susan mentioned made her cookies greasy. I have not experienced this and have used that recipe as my centerpiece Christmas cookie collection for years.

POLC, I actually think it's a thing with me. People love those cookies. I love the browned butter flavor. I almost get an oily, juicy mouth feel. Not describing it very well. Almost like I've made the cookies with oil. I was thinking of trying browning the butter and letting it cool to almost solid, but not quite. I never did try that though. I switched to the melt until creamy method.

I've tried letting the butter cool to room temperature and then creamed it with the sugar and it works pretty well. You don't quite get the super chewy/gooey texture, but they're still nice and soft. Something that might help, with anyone experiencing lacing or butter not emulsifying, is to chill the dough thoroughly before baking. It'll keep the butter solid for longer and keep the texture and shape a little tighter. Another thing, with this recipe in general, is not to skip the mixing and resting period. Its tedious, but its what really makes the emulsion successful between the butter, sugar and egg. Just be sure not to mix it too vigorously, or the overmixing of the egg will cause the egg to rise and collapse.