I posted last night about all the issues I had with the Cheddar Jalapeno Bread and went to the hardcore bread-bakers on the Cooking Light forums. This is what one user posted, and I'm pretty sure this is what happened. It's good to know for the future:
Flour varies from batch to batch in its moisture content. If you make the dough by the recipe exactly and it is much too wet, then you can add flour, a little at a time when kneading, to get the consistency back to normal for your recipe (assuming you know what the normal texture should be).
If the dough was too wet to start with, and you allowed it to rise for the recommended time, then it likely "overproofed". This means the yeast, in the wetter environment, were more productive and made more bubbles of CO2 gas than the dough could support during baking.
When you bake it, these busy yeast make too much CO2 gas in the pan, giving you a big bubble at the top and dense bread at the bottom.
My Laurel's Kitchen cookbook says "Overproofed loaves will be holey at the top and dense on the bottom, and may even collapse."