It is apparently a replace and an escape issue.
component.addOperation("CreateShortcut", "@TargetDir@/ArramgeApplication.exe para1 para2", "@StartMenuDir@/Arrange Application.lnk", "workingDirectory=@TargetDir@", "iconPath=@TargetDir@/Manager.exe");Creates the installer and creates also a link and adds the two parameters.
component.addOperation("CreateShortcut", "@TargetDir@/ArramgeApplication.exe @TargetDir@ para2", "@StartMenuDir@/Arrange Application.lnk", "workingDirectory=@TargetDir@", "iconPath=@TargetDir@/Manager.exe");Creates the installer, but fails when trying to create the lnk.