I've taken a look at the AdaFruit library. Unfortunately, it does not obey the protocol shown in the MAX6675 datasheet. It's holding the clock line high instead of low between conversions, and taking the clock low before reading the first bit, instead of reading the first bit after taking CS low and before toggling the clock. It's not clear from the datasheet that this isn't allowed, but it might perhaps cause the MAX6675s to get out of sync with the clock when you are reading more than one of them; and that would explain your bad readings.