If the mig.prj file was originally created using the "Fixed Pin Out" mode and a pin was selected for sys_rst, then that same pin site and IOSTANDARD will be used after generating the updated design and UCF using the "Verify Pin Changes and Update Design" flow. This may still occur even if a pin location was not selected during the "Verify Pin Changes and Update Design" flow.
Customers can work around this by manually changing the pin location and IOSTANDARD in the newly generated UCF file.This will be fixed in the MIG7 Series v1.4 13.4 release.