Vladimir,
Apologies for the long delay.
On ICEv2, an external buffer is added to avoid conflict between SYSBOOT and other signals(PRU MII, GPIO etc). On power up, the buffer will be enabled by default and the SYSBOOT signals will be driven to the chip. We need to explicitly disable the buffer after power up to drive other functional signals multiplexed on the pins. The buffers are controlled using PRI_MII_CTL/GPIO3_4 pin. So you need to disable the buffers using GPIO3_4 to have the GPIO2_12/12 (GPMC A18/A19) take effect.
So adding these in the flasher(during initialization) should resolve this issue -
GPIOInitialization(3);
GPIOSetOutputPin(3,4);
GPIOEnableDisableOut(3, 4, 1);
Additionally, you would need to set the pinmux of GPIO3_4 to the correct mode as well.
Regards,
Vinesh