OK, I've now run into problems, too. As reported, I had good readings on multiple TCs, but since made some code changes, and moved from the Arduino IDE to Eclipse. Now I only get a good reading on the first call of Adafruit_MAX31855::readCelsius() in a loop. That's even true for a single TC: calling readCelsius() twice returns zero on the second call. But when I upload the older sketch from the Arduino IDE, all temps come back on.
Adafruit's 'serialthermocouple' sketch reads the temperature from the board twice in a loop (celsius and fahrenheit). I'll try their code in Eclipse next.
A bit of a head scratcher at the moment.
Holger