Bagel-Consistency Issue: Sometimes Flat and Sometimes Perfect

I have a problem with my bagels coming out inconsistent, namely, some are flat (not desired, in this case) while others are puffy (preferred). I used Peter Reinhart's trusted recipe from the Bread Baker's Apprentice.

I uploaded an album so you kind people here can possible help me diagnose the problem. I photographed some of the steps in the bagel-making process in chronological order: (1) pre-boiling/after 24 hours of proofing in the refrigerator, (2) after boiling, and (3) after baking. Note that I tried my best to keep the controls (temperature, proofing time, etc.) the same for the two batches. Here's the gallery: https://www.dropbox.com/sh/68yh3h1qypvh8md/64BdOcNlzc.

I'm going to provide captions for each of these images:

1. Side view of BatchA after 24 hours of proofing. This was how they looked right before I plopped them into boiling water to cook.
2. Top view of BatchA after 24 hours of proofing. Still lookin' pretty good and puffy.
3. Top view of BatchA after putting each side in the baking-soda-laced water for one minute.
4. Side view of BatchA after the water bath.
5. Another view of BatchA after the water bath.
6. Yet another of BatchA.
7. BatchA after baking for 5 minutes. They look pretty good—I'm pretty happy with how they appear.
8. Side view of BatchA.
9. Side view of BatchA.
10. OK, here's BatchB. See how they're a bit flatter? I made this batch pretty much in the same exact conditions as BatchA. I'm a bit unhappy about how some of the bagels came out flat. 
11.  Side view of BatchB. See how there are some blisters in the bagel near the bottom-right corner? Not sure what that's about, but I'm going to guess it's due to the coarse-salt topping I put on it. There are some bagels in this batch that are puffier (the poppyseed one, for instance), and some that aren't as much (the rest!).
12. Side-by-side comparison of BatchA (left) to BatchB (right). Even though everything was made in the same conditions, they came out looking quite different.

Any ideas, friends?