There is a known problem with the Convert Programming files conversion of the SRAM Object File (.sof) from the Quartus® II software version 12.0 through 12.1sp1. The Disable EPCS ID check was enabled from version 12.0 through 12.1sp1, which caused the problem with link training and loading of the core image.
To wor karound this issue in the Quartus II software version 12.0 through 12.1 sp1, go to the Advanced tab of the the Convert Programming Files window and check the checkbox labeled Disable EPCS ID check.
In the Quartus II software version 13.0 and beyond, the Disable EPCS ID check is correctly set to disable.
This problem is fixed in the Quartus® II software version 14.0.