Depending on the version of Ultiboard you have, activate the spreadsheet view and you'll see under the "nets" tab that the layers are set for binary 10 it should be 11.
This is a problem with the transfer function of version 10. It is supposed to be fixed in 10.1.....but sadly it is not.
If you don't have spreadsheet view, go to the netlist editor under the tools menus and click on the misc tab and make sure both top and bottom layers are selected for EACH net.
that will solve your problem