I'm sorry but the game is doing exactly what it's supposed to do.
The New Game+ option only works twice, so after beating Zeromus for the third time the game is officially over, and you can no longer replay the game with the Augements you had etc.
This is basically to stop you from getting the Limit Break Augement too many times, but also to balance the game. Sorry, but if you want to play it again you'll have to completely restart.
Bookmarks