This is likely due to the code not using a delegate to initiate the application. 
Example delegate:

#import "AppDelegate.h"
#import "yourapp.h"
@implementation AppDelegate

- (void)applicationDidFinishLaunching:(NSNotification *)aNotification
{
    // Insert code here to initialize your application
    [_window setAlphaValue:1.00];   //etc. as needed
}

- (void)applicationDidBecomeActive:(NSNotification *)aNotification
{
    [_window setAlphaValue:1.00];
}

- (void)applicationDidResignActive:(NSNotification *)aNotification
{
    [_window setAlphaValue: _controller.alphaState];
}

- (NSApplicationTerminateReply)applicationShouldTerminate:(NSApplication *)sender
{
    return NSTerminateNow;      //NSTerminateCancel
}

- (BOOL)applicationShouldTerminateAfterLastWindowClosed:(NSApplication *)theApplication
{
    return YES;
}
@end