Just to add some more detail to this.
Running is_active_widget via the ‘init’ action, It looks like is_active_widget doesn’t work when you are using Jetpack’s widget visibility.
Stepping through the code for is_active_widget I noticed that widgets that should appear conditionally (and does appear on the page) are missing from the array that represents the active widgets for the particular sidebar it’s actually in (so are not returned as being active by is_active_widget).
It could be there is a more appropriate / later action that we should hook into to check widget visibility when Jetpack is installed?