Thanks to all who commented regarding Walgreen's pseudoephedrine tracking system, as well as several commentors who explained that the law is a little different in other states.
Your comments made it very clear to me that the problem lies in my own company's system for tracking pseudoephedrine. It's glaringly obvious that our paper log book is not sufficient to ensure we properly follow the federal law (regardless of how dumb I think that law may be).
I plan on bringing the issue up to my superiors and seeing if I can get anywhere with it. My guess is no, but it doesn't hurt to try.