Make sure that your board has proper termination on the JTAG lines.
Scope the voltages on the JTAG plug and make sure they are stable. Use
the mouse PS2 port, not the keyboard one, for the cable power. Make
sure you have updated chipset drivers. The odds are that your parallel
port controller is made by Intel. I wouldn't run any version of ISE
older than 6.2.3. I noticed some fixes in the 6.2 service packs. Make
sure the device manager shows that it is using the ECP driver and set
it to use an interrupt if one is available, which it should be.

If all of the above appear correct, then recognize the truth: there is
no spoon. The fact is that the DMA mode for the parallel IV stuff has
never worked worth a crap for me. The impression I got from support
when I called about it was that they get an aweful lot of calls on the
topic. The fact that they charge $500 for their USB cable is BS. They
do that because they have a monopoly on the item and use the
frustration caused by their parallel cables to drive the market.