Repository disappears after Ubuntu installation

I'm experiencing a problem with UCK, I've added three repository and their related secure keys through Synaptics during costumization procedure and all result to be saved correctly.
Next I have installed my custom ubuntu with WUBI and I've noticed that two repository previously added, are not present, only third repository is listed.
I've tested my ubuntu custom as live CD and in this way all added repository are available.
Am I doing something wrong?
This is a UCK bug or a ubuntu installation procedure bug?