Xilinx advertises that RHEL6 64b is a supported operating system for their Vivado tools suite. We love Vivado, but join the rest of the world in lamenting that support for the USB JTAG drivers under Linux in general and RHEL6 64b in specific is rough. We strongly suggest that if you too are having these issues, you file a webcase with Xilinx, and work with them to resolve your particular problem.
Sometimes you have to go a little outside the box to get something done; and that is what we just went through last night on our own, in order to get USB JTAG connectivity with Vivado 2012.3 and RHEL6 64b. First, we followed the well-known workaround that our Stanford friends list here, the third question down.
That didn't quite do the trick as we were still seeing 03fd:00d and not 03fd:0008 in response to lsusb. This is because /sbin/fxload does not come with RHEL6. I struggled in building it from sources and eventually gave up by finding an RPM pointed to here.
Cracking that nut got us to 03fd:0008 with lsusb and made Vivado (and Impact) functional.
At least one annoying USB related hurdle remains. The newer on-card USB adapters on the VC707 and KC705 do not work this way: you have to use an olde-timey USB/JTAG ribbon cable dongle and plug to the JTAG header. Interestingly, the older ML605 does work. And all the boards talk just fine with Win7 64b.
As others observing these Linux USB/JTAG issues with Vivado clearly and calmly file well-written webcases, Xilinx will have the data they need to make USB/JTAG as awesome and functional as the rest of the Vivado suite.