When setting the Bitgen option to persist the configuration interface (i.e., -g persist:yes) it appears that the configuration pins are not persisting after configuration is complete.
Setting the persist option to "yes" does not have any effect in 7.1.03i. This problem affects every architecture.
This problem has been fixed in the latest 7.1i Service Pack available at:
The first service pack containing the fix is 7.1i Service Pack 4.