Sorry that I was not able to get back on this earlier.
I tested upload from WordPress iOS (iPhone app) and Android app, and they didn't work with Custom Upload Dir (and probably other plugins too). The images were uploaded to WP default upload folder. I also tested from Windows Live Writer, the images were uploaded to WP default folder.
I guess this has to do with the way tools (iOS, Android apps and WLW) handle image upload. Hopefully someone will come up with tools that can organize media in better way. I am now stuck in between (1) hang on to WP editor to get the beauty of Custom Upload Dir plugin, and forget about other tools, (2) live with different ways different tools organize my media. Sigh.
Thanks for this great plugin again.