To work around this issue, remove the entries from the project file and re-run the ise_flow.bat file in the par directory.
verilog work ../rtl/.inotes
verilog work ../rtl/.pnotes
This issue only affects designs running the ise_flow.bat script file for a Windows generated Spartan-6 MCB design. Designs running on Linux or using an ISE flow will not be affected by this. The issue with the ise_flow.bat file on Windows will be resolved in MIG 3.5 (available with MIG 12.2). Until this time, the above noted work around is required.