Not sure if this is what's going on with your setup but...
When I originally ran thew second instance of the iCamSource software on my Mac Mini, it came up with a preference window containing all the same info as the first instance of the iCamSource software. When I changed the details, it linked up to my second camera.. But it did initially look like it was just opening the same pref window as the first instance.
You could also check that there are two little camera icons on the menu bar (over on the right hand side with the time machine, bluetooth, speaker, etc. icons). If you see two icons then you do have two instances running.