Note that there's two different 'messaging' systems at play, which causes lots of confusion, unfortunately.
system.util.sendMessage is the older, not-Perspective-specific, bus that was 'overloaded' to allow messaging to entire Perspective sessions. The handlers for these messages are defined in 'Session Events', and as Phil noted - not generally suitable for participation in the project inheritance scheme currently; all your handlers, of any type, are all managed by a single project resource, so inheritance is "all or nothing". This is a limitation that we're going to address in 8.3, but worth noting right now.
system.perspective.sendMessage, and the component messaging action, meanwhile, are the limited to Perspective message handling system. The handlers you define for these messages are those on individual Perspective components and views.
In other words: a system.util.sendMessage broadcast with a target of a specific session will not interact with a view or component message handler, even if it's set to 'session' listening scope.
That complication and/or the tricky interaction with project inheritance may be at the root of your issue here.