The -5V regulator LT1931AES5#PBF (IC13) shutdown pin is currently pulled low with a 30k resistor.
This pin is active low. To enable the regulator, a voltage bigger than 2.4V must be applied (LT1931 datasheet).

It might not work as the FPGA Vohmin with VADJ=2.5V can be as low as 1.9V in the worse case.
See Spartan-6 FPGA Data Sheet: DC and Switching Characteristics pages 8 and 10.

The shutdown pin should be pulled high to +12V instead. As for the 1V8 regulator LT1763IDE-1.8#PBF (IC9).