You don't need to create the window property since it is already available for NSWindowController subclasses. Maybe that causes the problem.
Also your init method contains a lot of code that doesn't belong there. Remove
[self loadWindow];
[self showWindow:@"Log Navigator"];
[self.window makeKeyAndOrderFront:nil];
as well as replace
self = [super initWithWindowNibName:@"LogNavigatorWindowController"];
with
self = [super init];
You may want to remove the init method at all, since you don't need it in your case.
and move
[self myDirectoryLogFunction];
to the windowDidLoad method.
Also always check that the code for instantiating the window controller (in your case from the app delegates didFinishLaunching: ) is called. Sometimes it helps to create a new project and test there, if you may have changed too much within the original project and by accident removed delegate connections or similar.