Did you visually inspect the pins in the ECU connector? It's possible that the pin got bent and therefore is not sending or recieving a signal from the wire harness? Stranger things have happened. It's worth looking into rather than buying a new ECU. Also, when they wired everything up, did they cut the ECU wires to splice the eManage harness in, or did they just remove the wire cover a little and then wrap and solder? It's possible that there is just a bad connection in the wire going to the ECU?

my $0.02