SOPC warning- Quartus 12.0-

Hi, you are new to NIOS II, aren't you ?

SOPC will be unsupported. It is replaced with QSYS, quite similar. Both get still bugs (path, script, missing...)

Do you work with an Altera developpment board ? DE2-2C35 ;-) ?

--- Quote Start ---

cpu_0:Custom Instruction components can be edited through the component editor

--- Quote End ---

could you post you SOPC (image or file) ?

--- Quote Start ---

(says Leaving target processor paused)

--- Quote End ---

After programming flash, it is normal. You can "start" the processor by :

resetting your board, then the proceessor will boot, usually, at the boot sector in a Flash memory

entering "nios2-terminal -g" something like that in a Nios Shell.