There is an error in the board layout for the Gallop43 expansion board here:
http://pubs.gumstix.com/boards/GALLOP43/
 
We just did a design based on that board and schematic file and ended up with a PCB that's totally shorted out.
 
The inner layer 2, named $GND is incorrectly marked as a "Signal Layer" which means it will short out any vias going through that layer:
http://www.cadsoftusa.com/training/faq/#17
 
Even without changing the design at all, it produces a PCB with vias incorrectly shorted to the GND layer.
 
To fix this problem, go to the hide/display layers, double click on the $GND layer, uncheck the "Supply Layer" checkbox and re-ratsnest.