////////////////////////////////
2) If I work with both the blaster cable and the device cable connected, the system can transmit data from PC to device successful, but when I try to send data from device to host PC, it show me a timeout error.
//////////////////////////////////
This behavior is result from hardware design.
Clock 12 MHZ goes from byte blaster to the ISP1362.
When blaster cable is not connected 12 MHZ clock is absent !!!!
And ISP1362 not worked.
So decision is to provide clock 12 MHZ from Cyclone II pll.
I have implemented pll with clock into FPGA and connect it to the pin VGA_HS.
On the board I solder wire between VGA_HS and signal side of the capacitor C54. Also I have moved away resistor R126.
So ISP1362 work without blaster cable to be connected.