I’m also having this same issue and have opened a support ticket.
The GPON module was working fine in my RB3011 but causes the health failure in my ccr2004 on the latest stable and testing releases.
The supout shows that the I2C bus is likely locked up as there are nothing but time outs waiting for the bus to be ready. Not sure if it relates to the single byte read request here:
http://forum.mikrotik.com/t/request-support-i2c-sfp-sfp-secuential-singlebyte-reads-to-obtain-transceiver-details-from-eeprom/142454/1