If they are using the standard Ducati Mathesis test box, and the ECU has an FIM upgrade chip, then the box will not be able to talk to the ECU. If the ECU wasn't working the bike wouldn't run.
It sounds like you may need the TPS setting adjusted to sort out the fuelling. This can be checked with a multimeter. Here is how..
http://www.bikeboy.org/ducati4vthrottleb.html
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