You can enable the DO_DISABLE_ISP_CLAMP procedure when executing JAM or JBC file, to bypass the ISP Clamp and perform the Real Time ISP operation.
If using the quartus_jli executable, the command would be:
> quartus_jli -aprogram -eDO_DISABLE_ISP_CLAMP -eDO_REAL_TIME_ISP .jam/.jbc
If using the JAM STAPL player, the command would be:
> jam -aprogram -dDO_DISABLE_ISP_CLAMP=1 -dDO_REAL_TIME_ISP=1 .jam
If using the JAM Byte Code player, the command would be:
> jbi -aprogram -dDO_DISABLE_ISP_CLAMP=1 -dDO_REAL_TIME_ISP=1 .jbc
This issue is scheduled to be fixed in a future version of the Quartus Prime software.