My pitfall was losing a few invisible rectangles. Let me explain. (If you are not an aspiring Adobe Illustrator amateurs like myself, the following details may not be particularly exciting.)
In order to define the bounding box for the repeating design, I had to create a rectangle that has no fill and border. Of course, you cannot see a borderless colorless rectangle unless you hover over its edge or select it. In the process of creating my pattern multiple times in the same document, I inadvertantly left a few of these rectangles behind. Since a design for a pattern can only have one bounding box, these multiple rectangles were no doubt confusing the tool. Last night as an act of desperation I started browsing through the layers in my pattern, and that is how I discovered that I had a few more invisible rectangles than I expected. Once I deleted all but one, my pattern generated correctly.
