One thing, I wouldn't have 512 channels setup, the Alphapix can't handle that. If you ever have to "rollover" to another universe you will have issues. So, set to 510 or just set to what you actually have.
It looks like the main problem is setup. On the tree you have string #1 set to start at 4097, #2 at 4247, #3 at 4397...., however, in the setup universe #1 is 4097, #2 is 4609, #3 5121. So, this will not work. I'm not schooled on the Alphapix so not sure on the options, but I would think you could set to contiguous. Or, change the string start channels in the model to what you see in the setup, so string #1 would be 4097, string #2 4609, string #3 to 5121. All of the info is right at your finger tips. Print the layout off if you need to.
James