when you say LS ECU, we're talking a chevy LS harness. yes?
If so, you can get a pinout to trace contenuity of the injector wires on lt1swap.com. It will tell you what pins on the PCM connector go out to the injectors.
I have trouble believing that the issue would be in the PCM. It COULD be in the tune (not likely). My bet would honestly be that its in the harness or the connector.
Select the appropriate link based on the year of PCM you're using.
http://lt1swap.com/2000harness.htm
PCM Connector Pinouts 99-02 - PCM Pinouts for 99-02 BLUE / RED PCM connectors. Similar BETWEEN 99-2002.
PCM Connector Pinouts 03-07 - PCM Pinout for 03-07 BLUE / GREEN PCM connectors. Similar BETWEEN 2003-2007.