This might be at least part of the problem. In Charliplexing.cpp:
#define MEASURE_ISR_TIME
#ifdef MEASURE_ISR_TIME
uint8_t statusPIN = 19;
#endif
The Chronodot is an I2C device which will therefore use ANALOG pins 4 and 5 for the I2C communication. These are also known as DIGITAL pins 18 and 19 and the above code allows the Charliplexing stuff to use analog pin 5.
Try commenting out the define and see if it makes any difference:
//#define MEASURE_ISR_TIME
Pete