The DS3231 may be stopped for some reason other than your code.
Control Register (0Eh)
Bit 7: Enable Oscillator (EOSC). When set to logic 0,
the oscillator is started. When set to logic 1, the oscillator
is stopped when the DS3231 switches to VBAT. This
bit is clear (logic 0) when power is first applied. When
the DS3231 is powered by VCC, the oscillator is always
on regardless of the status of the EOSC bit. When
EOSC is disabled, all register data is static.