Quick breads rise while the baking powder is working....if they rise too much, they will collapse and since there is nothing left of the chemical which caused them to rise....they will be flat.
You were lucky! in 20 minutes they didn't deflate.
Linda C

Why it worked. And when it won't:

Question: What Is the Difference Between Baking Soda & Baking Powder?

Answer: Both baking soda and baking powder are leavening agents, which means they are added to baked goods before cooking to produce carbon dioxide and cause them to 'rise'. Baking powder contains baking soda, but the two substances are used under different conditions.

Baking Soda

Baking soda is pure sodium bicarbonate. When baking soda is combined with moisture and an acidic ingredient (e.g., yogurt, chocolate, buttermilk, honey), the resulting chemical reaction produces bubbles of carbon dioxide that expand under oven temperatures, causing baked goods to rise. The reaction begins immediately upon mixing the ingredients, so you need to bake recipes which call for baking soda immediately, or else they will fall flat!

Baking Powder

Baking powder contains sodium bicarbonate, but it includes the acidifying agent already (cream of tartar), and also a drying agent (usually starch). Baking powder is available as single-acting baking powder and as double-acting baking powder. Single-acting powders are activated by moisture, so you must bake recipes which include this product immediately after mixing. Double-acting powdersreact in two phases and can stand for a while before baking. With double-acting powder, some gas is released at room temperature when the powder is added to dough, but the majority of the gas is released after the temperature of the dough increases in the oven.

How Are Recipes Determined?

Some recipes call for baking soda, while others call for baking powder. Which ingredient is used depends on the other ingredients in the recipe. The ultimate goal is to produce a tasty product with a pleasing texture. Baking soda is basic and will yield a bitter taste unless countered by the acidity of another ingredient, such as buttermilk. You'll find baking soda in cookie recipes. Baking powder contains both an acid and a base and has an overall neutral effect in terms of taste. Recipes that call for baking powder often call for other neutral-tasting ingredients, such as milk. Baking powder is a common ingredient in cakes and biscuits.

Here is a link that might be useful: From About.com

Well okay then! Thank you both so much for the good information. Well Linda presumably that's why Mom always just put her quick bread loaves in the oven. Wasn't smart to let them languish on the counter.

Thank you barnmom. I'll read through that. I'm happy I asked.

Kate

I recall seeing on some cornbread muffin recipes: "(For Maximum Crown On Muffins Let Batter Rest For 3 Or 4 Minutes"

Good to know. I like making Cornbread also so I'll try it. Four minutes or so should be pretty safe from the sounds of it. Thank you.

Kate

I'd be more inclined to think that something else caused your second batch of muffins to be higher. Perhaps you didn't realize that you filled the pans a little higher. Or maybe the oven wasn't thoroughly preheated when you put the first batch in. But according to recipe science--as others have explained, the second batch should not have risen higher (if all things were equal. I am a bit curious? Why let them rest on the counter at all? Why didn't you just put them in the oven when you filled them? Does your oven have only one rack?

Along with what azzalea posted, I'm inclined to put aside the "resting" theory. Not having your oven preheated to baking temperature for the first batch is probably a better guess. Or your eggs were cold in the first batch, and had warmed by the time the second batch had been placed in the oven. Food science indicates cold eggs reduces volume.

Double-acting baking powder reacts twice - once when it's mixed with a liquid (carbon dioxide bubbles form), and again when it hits the heat of the oven. So it's very important to quickly mix, pan the batter and bake immediately. When using a chemical leavening, always have the oven preheated before you mix your ingredients together. Or as I was taught, "never let the cake batter sit waiting for the oven to get hot".

I'm not sure about the "maximum crown resting time on a muffin" suggestion. That's a new one....

So what does a blue-ribbon winner of a muffin look like? As a trained foods judge, it's symmetrical with a slightly rounded top. The surface is pebbled or bumpy. The volume of a freshly baked muffin should be about double its size as uncooked batter, and it should feel light in proportion to its size. These characteristics indicate the leavens are well-balanced and have lifted the batter as high as possible just before it sets in the oven.

Balanced leavening? If there is both baking soda and baking powder in the recipe, soda is four times as strong as baking powder, but soda only reacts with an acid ingredient. The general rule is 1 to 1-1/4 t. baking powder per cup of flour and 1/4 t. (or a tiny bit over) baking soda per cup of flour in the recipe. More leavening may be needed if the recipe calls for a lot of heavy ingredients, like chopped fruit and nuts.

-Grainlady

I'm learning so much from all of you. Thanks so much for your informative posts.

I understand what is being said about how the second batch probably wasn't bigger from a rise now. Yes the eggs were cold on the first batch probably. I put the recipe together quite quickly and the batter itself was a bit cool from the cold apple, zucchini and eggs in it.

I did not put all the muffins in at once as both pans weren't ready at the same time and I wasn't sure my two pans would fit. Like I said I was really punting on making what is normally three loaves of bread (in this recipe) into muffins instead. The oven was pre heated but yes I do only have one rack. I probably need to invest in another one as I have been cooking a lot more this summer and a second rack would be most helpful.

Really appreciate your posts. Thank you.

Kate