I have tried several different combinations of these with no change.
The Due has two sets of I2C pins, IIRC. Can you connect the RTC to the other pins, and modify the library to use the other I2C instance?
Or, perhaps you could use the Report to moderator link, and asked that the thread be moved to the Due part of the forum, where you might get better answers.
Also, could you post a link to the VS1053SdFat library? Perhaps a clue will present itself.