It appears on Friday that they were churning out batches and as soon as they were done with a batch, the next set of choux were not quite ready to be filled. I went towards the end of the day on Friday, and I got there right in the middle of one of those lulls. They then determined that the next batch was ready, and out came a bunch of happy folks with their boxes of puffs. I had to wait through 2 cycles before I got my pack.
What's up with that? Even at the teeny tiny Beard Papa's in Japan, I've never had to wait for the choux to be ready. They don't fill until you order them, but the whole operation is very efficient and there are always enough choux ready to be filled, no matter how long the line.
The only things that have ever had longer waits are the mochi choux (which they only make at certain times of the day, but they're seasonal, anyway, so they rarely have them), and other specialty products.