Thanks for the second pair of eyes and the tips on the delay and debug. I didn't know about those.
I also should have explained that my issue's not so cut and dry. The checkboxes are located on a pop-up that appears after clicking a button on the page. So when the page loads, the autofill rule fires correctly (via the debug output) and I can go inspect the input elements before clicking the pop-up button. When I inspect them before opening the pop-up, the class attribute on both of them shows as "ng-untouched ng-valid
ng-not-empty ng-dirty ng-valid-parse" but when I open the pop-up, the second input element's class attribute changes to "ng-untouched ng-valid ng-dirty
ng-empty". So it seems like the second checkbox clears itself after I open the pop-up. I guess it might be best to have this rule fire on a hotkey since I don't think it can deal with this pop-up scenario.