Did a bit more research on the download issue and found that the problem is widespread. In fact, it appears that only The Guardian (and perhaps the NYTimes) don't suffer from the halted download problem because, presumably, they manage to support the unattended background downloads consistently. Virtually all of the Conde Nast publications (e.g. New Yorker, SI, Vogue, Wired, etc.) have the same problem.
From what I can tell, the problem comes about when the unattended background delivery feature fails. This process only works when an iPad is on wifi so if an iPad is wifi only and not connected or is on a 3G network rather than wifi, the automatic background download won't, of course, occur. In addition, it appears that even if these conditions are passed, the automated background download may fail due to network contention or server overload. (A task running in background has 10 minutes to finish its task. If it doesn't complete in that time, it fails completely.)
The result is that the Newsstand icon for a publication may be updated (indicating a new issue has been delivered) even if the download of content fails. In that case, it's up to the user to initiate the download and if the user leaves the app in this situation the "background completion" feature is disabled (or doesn't exist.) The download stops and must be restarted from the beginning.
I suspect that the engineers who coded the apps for the various publications that are failing thought they were doing what they needed to do to support background downloads. (That, after all, was the main objective of the Newsstand subsystem.) The problem is what I suspect is a failure to account for failed downloads when the unattended background process fails. I also suspect that Apple is aware of the problem and may update Newsstand to avoid it. By the same token, however, I suspect that it will require an OS update to fix it since Newsstand is not an "app," but a feature of iOS 5.
The url below (especially the comments section) is probably the best documentation of the problem.
What’s the Point of Newsstand Automatic Background Downloads?