Hopefully this information might save someone else some time.
If you're using ISE6.2 under Linux, and want to use an old programming cable, such as the Parallel Cable III (DLC5). you need to compile your own Linux drivers.
This Answers Database record has the info:
Here's a few pointers.
Make sure that the version of kernel you are running, matches the kernel source you have installed. The xilinx makefile uses uname -r to find this out.
So do uname -r at a command line, and check that the kernel files in /usr/src match this and the files in /lib/modules match too.
If they don't, try doing an update of your system, updating both kernel and kernel source (I'm a SuSE user, and in this case use the online update). Then REBOOT, this makes sure that the version uname returns matches that installed.
Hope this helps Andy