Yes, while the movie is playing, I and everyone else are able to start the pop-up menu. Regularly, movies with IGS menus are having only the pop-up menu and a menu that starts when you call it, regularly just one picture to select certain extra features.
As you can see here:
Codec Bitrate Description
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MPEG-4 AVC Video 0 kbps 1080p / 23,976 fps / 16:9 / High Profile 4.1
The menu is not in the same container as the movie. Before starting this guide I've tested on this movie that I have in my personal collection: Wedding Crashers 2005 Theatrical and Uncorked version.
Codec Bitrate Description
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VC-1 Video 0 kbps 1080p / 23,976 fps / 16:9 / Advanced Profile 3
As you can see, the same principle applies. I wouldn't have written that in the guide if the method wasn't tested.
I will borrow a BD with an IGS menu and I'll test some more to see if I can replicate your lack of pop-up menu. It will help me if I know the name of the movie you are trying to edit. Maybe I have it, or a friend has it and I can do further tests. Also it would help me to know if it is the US or EU version.
Later edit: As I promised, I've done some further tests. Everything is functional, I even replaced the clpi file ( normally it isn't done ) for you to see that is possible to have a pop-up menu. With the java discs is even more easier. In this test I've removed all audio streams and left only one subtitle. So there can be no doubt that is a real test.
Original:
Edited:
As you can see, they both have the pop-up menu while the movie is running. Sorry for the quality of the pictures.