As of ISE 11.1, an IP core generated in Project Navigator is stored in a ipcores_dir subdirectory by default.
XST's default behavior is to look for core netlists in the main project directory.
Project Navigator is NOT automatically specifying the XST -sd flag for the generated cores. Thus, XST blackboxes the cores and cannot read them for any kind of preliminary timing data, etc.
You can work around this issue by manually specifying the Cores Search Directories (-sd flag) under Synthesis Options to tell XST where to find the cores.
This issue is resolved in the ISE 11.3 update.