The issue is with the registry location used to locate user libraries.
To work around this issue, copy the ECS registry in ISE 10.1 to paths with 10.1i. To do this:
1. Go to Start -> Run.
2. Type regedit and press Enter.
3. Go to the following key: HKEY_CURRENT_USER\Software\Xilinx\ISE\10.1\ECS
4. Right-click and choose Export.
5. Save the file.
6. Open the .reg file in a text editor.
7. Replace "10.1" with "10.1i" (use the text editor's Replace Functionality).
8. Save the file.
9. Go back to the Registry Editor and select File -> Import.
10. Select the file saved above.
Run Synthesis on the design; the User Libraries should be read correctly.
This problem will be fixed in ISE 10.1 Service Pack 3.