First thing that needs to be done is to see what the problem is with cylinder #1. If the same fault is suspect, then it needs to be checked with either an oscilloscope on the ECU output, or a Noid light, not by random swapping.
If ECU #1 output is now faulty, then the ECU may well have to go back to ECUtesting again. Not sure if they will fix under warranty, perhaps best not to go into too much detail... I'm a bit surprised they didn't point out that the offending injector should be replaced.
If the ECU output looks good, then the injector needs to be checked and/or replaced. A simple resistance check against a new/good injector will probably show up a faulty one.
Note that the problem with these injectors is electrical, not mechanical.