This issue is caused by the constraints embedded in each netlist not being merged correctly by XST.
To work around this issue, follow these steps for an example core named 'xps_usb2_device_0':
1. Change in to the projects implementation directory for the core:
2. Edit and save the UCF file to eliminate duplicates in all timegroup and timespec names; this includes all strings that begin with TNM_, TG_, or TS_. Use a text editor "search and replace" function to replace each with a core-specific version, such as TNM_0, TG_0, and TS_0. Backup this file for later use.
3. Merge the modified UCF into the NGC netlist file:
ngcbuild -ucxps_usb2_device_0_wrapper.ucfxps_usb2_device_0.ngc ../xps_usb2_device_0_wrapper.ngc
4. Continue with the XPS build process normally. Any changes to the controller parameters or a project clean require that all changes be re-made.