p.23 says "Note: If there is no signal at the digital input or if the signal is absent or corrupt, the EXT LED and rate LED will blink and the Eclipse will switch to the internal rate closest to the last valid external rate."
Can you confirm that CLOCK is set to DIGIN, and that "Dig-In" is set to RCA ? If so, it suggests that there is a problem with the digital input signal.
You imply that you are running at 48kHz – note that S/PDIF is not always reliable at higher sample rates.
