I wasn't questioning the cables integrity, but the integrity of the connections where the plug enters the jack. A small difference (<1mm) in one plug to another may mean the difference between grounding out the tip or not. I was suggesting that you manipulate the cables to see if they have different tolerances verify they aren't grounding out somewhere in the chain.
For example, say the cable you are using to go from pedals to amp has a slightly longer sleeve than the one that you have going from bass to pedals. It may work beautifully going from the Boss to the amp, but ground out on the EBS by being pushed in too far. I don't know that this is the answer to your problem, but I've had this problem with perfectly good cables. Try pulling one of your cables out of the EBS only slightly and see if you get some sound.
