Is the NSStatusItem contained in the PreferencesWindow nib? That might explain it, since you're loading the nib each time the button is clicked.
Also, is there a reason you need to recreate that window each time the button is clicked? Maybe you could only do it the first time?
- (IBAction)preferences:(id)sender {
if( self.windowController == nil ) {
self.windowController = [[NSWindowController alloc] initWithWindowNibName:@"PreferencesWindow"];
}
[[self windowController] showWindow:self];
}