@Clyde, this is a co-workers unit and he couldn't remember all of the details about it but I think that you are correct about it being a non official retropie image. It had a very out-dated version and when I updated everything is where the issue happened. I will talk with him at work Monday, explain what happened and let him know that I will set him up with an official copy.
Yes, I did what you said and I succeeded to lower boot time to 11 seconds for libretro emulator but only through autostart.sh.
However, non-libretro emulators still starts about 5 seconds faster through the rc.local script and I dont know what else I could do here.
It seems runcommand is a problem, because for some reason it refuses to start through rc.local properly...