In whisker-menu, items with categories that for whatever reason make the apps end up in the "Other" menu category, tend to disappear.  For me, the whole "Other" category disappears until a login/logout is done.  However, any favorites that point toward items in "Other" also vanish and do not return on the login/logout.

The behavior happens after a set amount of time, however, I can trigger the behavior by enabling "Show Menu Hierarchy".  "Other" should immediately disappear, as will the favorites.

wine apps are the most common to show up in "Other", but there is a linux-native weather data app called ZyGrib (in debian jessie repo) that also ends up there.