What synthesis tools are supported when using the partitions flow?
XST and Synplify Pro 8.8 or later, with compile points (see (Xilinx Answer 24870) for more information on compile points), are the only synthesis tools supported for use with the ISE partitions flow.
Other synthesis tools might allow you to include partitions using compile points, but Xilinx does not test partitions from other synthesis tools, and therefore, they are not supported.
You can include netlists synthesized using other synthesis tools as a complete partition within an XST design, but in order to do this you must use an HDL wrapper file and apply the partition to the wrapper.
If you have an issue using partitions with a synthesis tool other than XST, or Synplify Pro 8.8 or later and can recreate the issue using either of the two supported synthesis tools, please open a WebCase with Xilinx Technical Support: http://www.xilinx.com/support/clearexpress/websupport.htm.