With the same code, but the call to playMP3() commented out, does the program get the correct time from the RTC? --- YES it also gets the correct time if the music is not playing.
With the same code, expect the MP3 DCS, DREQ, and RESET connected to other pins, does the RTC provide the correct time? --- I have tried several different combinations of these with no change.
The shield has 11 Pins used
6 of them I do not define They are MISO, MOSI, RESET, VCC, GROUND, and SCK. These are on the ISCP Header, They are the Hardware SPI for DUE.