Don't know if this is a known bug or not but seems like in VA Outline and alt-m listing Visual Assist doesn't list functions inside functions. An example is this:
function test1() {}
(function() { function test2() {} function test3() {} })();
The list looks like this:
Auto-complete, however, does pick up on the functions:
Declaring functions inside others is a very useful way of achieving encapsulation, so it would be nice to have that functionality for Visual Assist. (Btw, the JSON notation of declaring member functions doesn't work very well too but I think there is a post about that already)