I think I've figured out that it's a problem with how the browser cache (or local storage?) is being set.
Any time I make a copy of an alert, I believe the browser caches the copied alert's conditions.
Subsequently, when I open the original alert – or even any other alert, the browser loads its cached version, which is the copied alert. As a result, this gives the impression that what I am seeing is the copied alert.
If I reload my browser (i.e. using Ctrl-R), the alert that I intend to open shows up with its correct conditions.