megafunctions problems

The short answer is, yes you probably need a license for the NIOSII processor if you are using SOPC Builder. There may be other IP cores besides the processor in your design, I dont' know. You can still use the time-limited version (usually called projectname-time-limited.sof but Quartus will only generate a "temporary" .sof file for your FPGA that will run for a limited time before quitting (sometimes the IP cores will run in tethered mode where they will run as long as you want if you keep the programming hardware connected between the board and your PC), but you won't be able to permanently program the board.