It may be that whatever follows the Eclipse is loading down whatever is feeding it.
Or, to put it another way, the Eclipse is acting as a buffer in normal use. When the Eclipse is set to bypass, it is removed from the circuit and you lose the buffering. You can probably confirm this by connecting directly, bypassing the Eclipse.
You can solve this either by resolving the (non Eclipse-related) loading issue, or by setting the Eclipse to DSP bypass.
