Description
A Stratix® V, Arria V or Cyclone V device may fail to enter user mode when configured over JTAG, if the .sof is generated from a Quartus® II project where a Configuration via Protocol (CvP) mode is enabled. This is because when you have CvP mode enabled and when you configure the FPGA over JTAG, it would then be necassary to write to the CvP Mode Control registers in the PCIe IP (via the PCIe link) after configuration is complete, to allow the device to enter user mode.
Resolution
To configure the device over JTAG, recompile the project with the CvP mode disabled, to generate a new .sof.