I'm afraid that you probably have to talk to Digi – if the Eclipse is showing the right sample rate and the EXT light is not flashing, it is doing all it can. But, make sure that sample rate conversion is off (Setup/digin/SR-CNV on p.26 of UM).
It is unlikely that changing the sample rate will noticeably affect the sound quality in itself. My guess is that you probably have a sample rate incompatibility somewhere.
Having said the above, there are many other things it could be:
1) You don't say what preset you are using – maybe it sounds the way it is supposed to ? Try using Preset 102, Thru Seriies
2) Maybe the level to or from the Eclipse is too high or too low ? Make sure all the green leds light on peaks and that the red one never does.