Well, I am not familiar with that particular board, but there are many things you can look into when it comes to your JTAG problem.
- Check the voltage of your VCC, make sure it has a good value for the board
- Make sure your ground connection is well connected and you don't have much impedance between the connector's GND and the boards GND
- Try other JTAG connectors and see if you see any difference in the detection of the devices.
- Try to run the IMPACT in debug mode. Capture the data and see if the patterns look OK
Also something that may not be JTAG related, is to make sure your V5 device has all the powers it needs, if there are any power problems, it may cause the JTAG interface to behave like you explained here. Also, look on the board and see if there are any switches or jumpers to chose different way of configuring the V5 device. This can be a big issues with multi-FPGA board, maybe the V5 is configured to be programmed from a controller or other devices on the board and the JTAG chain is not set up for programming.
These are just different thoughts, they may help you toward the right direction.
Found this on their site: User guide for the board
To reprogram the flash ROM (ST45DB16D, U11) for the control FPGA (Spartan-3A), attach the configuration cable to CN7. For configuration, use the provided mcs file sasebo_gii_ctrl.mcs. Reprogram the flash ROM (ST45DB16D, U4) for the cryptographic FPGA (Virtex-5 LX30) with the provided mcs file sasebo_aes_comp_lx30.mcs as well. Connect the configuration cable to CN4. To configure the FPGA immediately after reprog ramming of the flash ROM, cycle the power. Blockquote
This means you can't program the FPGA directly, you need to convert your bit file into MCS file and then load it into the FLASH memory on the board.