There are eight User LEDs. It seems that first four LEDs (D9, D10, D11 and D12) are not connected.
I checked the schematic and the pin assignment of CPLD, but the pin corresponding to each of the LEDs (LED0, LED1, LED2 and LED3) cannot be assigned in CPLD.
http://processors.wiki.ti.com/index.php/AM335x_General_Purpose_EVM_Board_Design_Files#Rev_1.2A
http://processors.wiki.ti.com/images/f/f0/Am335x_gpevm_pinuse.zip
Can the LEDs (D9, D10, D11 and D12) not be used?
Best regards,
Daisuke