This problem has been seen on Windows NT 64 platform only (Not on Vista64 and 32-bit Windows platforms).
The issue is resolved in ISE 11.1
To delete a Flex license cache manually, do the following:
On Windows: delete the Registry key "HKEY_LOCAL_MACHINE\SOFTWARE\FLEXlm License Manager\XILINXD_LICENSE_FILE". On UNIX/Linux: delete the line beginning with XILINXD_LICENSE_FILE in the $HOME/.flexlmrc