I don't think he is trying to tell you he doesn't feel well. If that were the case he would still be screaming even if you were right there.
It sounds alot like seperation anxiety to me. Some kids develop that around 6 months.
Some questions you might want to ask your sister are: Does your sister have the same problem? Does he freak out when she leaves a room without him? Is she always at his side or in the same room with him? Does she just let him cry if she has to leave the room without him? How does she handle the situation?
I don't really know what to advise you to do though. My daughter never did this at 6 months. (she just started to do this a few weeks ago) What I do though is I try to get my daughter involved in something like playing with her toys or I will put her favorite cartoon on (I know 6 months is a little young for this, but the Baby Einstein videos are fabulous. They have classical music and images that kids like to watch. I would put one on if I couldn't get my daughter interested at anything else when she was young like this) and then tell her I will be right back. She still cries when I leave the room, but I always try to do whatever I need to do very quickly and by the time I'm done she is usually playing with her toys or watching the cartoon.
I hope you can find a solution to help you! It can be really draining to have to deal with a crying baby all day long.