which part of data in ethernet frame should be passed to CRC generator?

use the first option instead of auto analysis, and this will only run one time. Did you set any trigger?

You musn't cancel the IP plus messagebox, because all your unlicensed cores will stop working. To be able to use evaluation and signaltap at the same time, you need to run one of the two tools (signaltap or the quatrus programmer) separately instead of from the Quartus menu. You will find them in C:\altera\xx.x\quartus\bin (programmer is quartus_pgmw.exe, signaltap is quartus_stpw.exe). Then you can program your FPGA, keep the IP Plus window open, and use signaltap at the same time.