Launching iReport from a java application runs very well the first time, but it is not the case the second time, the third time, ...
To test it, I wrote a Java app that launch iReport when you click on a button. So the first time, iReport runs well, when if you close it and you click again on the button to launch iReport, it will not work any more (for instance, try to align some text with the specific IReport buttons alignment). Try several times, it only works the first time.
This test was made with iReport 1.3.3 and iReport 2.0.