Just shooting in the dark here.
// Test setting different digits
data[0] = display.encodeDigit(1);
data[1] = display.encodeDigit(2);
data[2] = display.encodeDigit(3);
data[3] = display.encodeDigit(4);
data[4] = display.encodeDigit(5);
data[5] = display.encodeDigit(6);
display.setSegments(data);
The above array might be the key.
Might have the sequence wrong:
// Test setting different digits
data[0] = display.encodeDigit(SECONDS % 10); //units
data[1] = display.encodeDigit(SECONDS / 10); //tens
data[2] = display.encodeDigit(MINUTES % 10); //units
data[3] = display.encodeDigit(MINUTES / 10); //tens
data[4] = display.encodeDigit(HOURS % 10); //units
data[5] = display.encodeDigit(HOURS / 10); //tens
display.setSegments(data);