It is working for me now after I ran the init_eeprom.sh. I am sorry that I may have misunderstood the Logi-bone quick start guide instruction --- I thought only earlybird boards needed to run that.
Thank you, Jonathan, Mike and Ribbox for all your time, advice/tip and help.
I noticed in your last post, you did "cd Logi-apps". In my case "Logi-apps" came with the logi ubuntu image. To get the updated apps, I did "git clone -b logibone https://github.com/fpga-logi/logi-apps.git", then I have a "logi-apps" directory (note the lower case L). I then use the "logi-apps", not "Logi-apps".
I don't know if this applies to your case or not.
I am not an expert on this. Just want to share my experience, in case it is helpful.