Faulty RS-485 device has irregular effect on neighboring devices in bus setup
I think to properly diagnose this you will need to eavesdrop with something like a FTDI rs458 converter, along with an oscilloscope.  With the scope you can see when a transceiver grabs and releases the line.  You may have to manually poll each node and review each response.  If you can pinpoint the module that is holding the line "down", see if its corresponding enable pin is actually held high.  If the line is not being held down, it could mean that two nodes are attempting to reply at once(atmega firmware issue).

Be sure that you have terminated the system with two 120 ohm resistors per repeater instructions.