The workaround is to increase the timeout count in the system console Tcl script. Here are the steps to implement the workaround:
1) Open the nios_phy_111.tcl file in the following directory:
2) Search for the variable MAX_PROC_LOOP and change it to 4000 as shown below. This variable specifies the number of seconds the debug toolkit will wait to hear back from the Nios sequencer before timing out:
# The maximum number of times we can go through the sleep loop waiting for the processor
variable MAX_PROC_LOOP 4000
3) Reopen the debug toolkit and connect to the Stratix V device. It may take several minutes to connect but it should connect and tell you which stage of calibration failed.