I have recently tried to install Xilinx 11.4 and have run into a standard exception error involving the System Generator generated perl script MasterScriptXXX.pl. This error has occurred on Ubuntu 8.04, 9.10 and Fedora 12. Xilinx support would not answer questions until I installed a supported OS (Red Hat Enterprise 5 or Suse Enterprise Linux 10). I tried RHE5 and the error went away and my design compiled. A possible free alternative is CentOS and is supposed to follow the same distribution cycle and carry the same packages and versions as RHE5, but I have not tried this and I doubt Xilinx would support it.
The cost of a RHE5 license is zero compared to say, a switch, so I think that's the option we're looking at here in Berkeley. Mark