I've been working with the new repeating command blocks lately and it seems that they SOMETIMES (not always) completely ignore a redstone signal if it's weak, like 10+ blocks away from the source. I'm not sure if this also applies to the other command blocks but I only noticed it with the repeating ones. Placing a repeater to strengthen the signal seems to fix the problem, but I still think this issue should be fixed.
Could you provide screenshots of your exact setup as well as the command used?