Checking out the project under a different name fixed things... What?!? I hate eclipse...
Orange question mark's in the gutter of flash builder 4.5 when looking at import statements or class references of an 'Added library'.
I'm not even sure this is an OSX issue or what is going on, but flash builder refuses to compile in (for the source editor at least) the library. Below is what your build path should look like when referencing a project.
But, this in turn causes the following orange question marks and inability to import new classes / use any code completion eclipse features for referencing library classes.
So, the fix (workaround) is to import the *.swc instead of referencing the whole project. I'm assuming there is something in my library project that flash builder doesn't like... Perhaps a design.xml in the root or some such thing, but...
Hopefully this will help someone else.