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There are problems with usage of XVC with ISE/Impact, when JTAG chain contains more than one chip. The problem is described here:
http://forums.xilinx.com/t5/Design-Tools-Others/iMPACT-XVC-broken-with-multiple-devices/td-p/496232
Probably it can be solved by tracking the TAP state machine and blocking the erroneous transaction as described here:
http://debugmo.de/2012/02/xvcd-the-xilinx-virtual-cable-daemon/
and implemented here:
https://github.com/tmbinc/xvcd/blob/master/src/xvcd.c#L146

There are also problems with operation with new Vivado tools. Problem is reported here:
http://forums.xilinx.com/t5/Configuration/Problems-with-XVC-plugin-both-in-ISE-Impact-and-in-Vivado/m-p/631321
and not solved yet.