It's that built in prey animal instinct that makes them run away. They look at you as this gigantic person. Give them time to adjust but they may always run away. I have had my Chatty for 9 months today and she still runs everytime I get too close to the cage or when I go to pick her up. But I have other pigs will come to the side of the cage for nose or chinny scratches. Some pigs just don't get as used to us big ol' humans as other pigs do.
Continue to give your piggies lap time. Its very important for bonding. Be careful though, as you see they can jump out of your arms quickly and hurt themselves. Try holding your piggy in a towel and then baby talk to her while you are petting her. Over time she/he will come to enjoy your lap time, just be consistant.
Sometimes my piggies get startled by noises that I don't hear, or sounds that I've tuned out. They all freaked out once when the futon couch sqeaked when I sat on it. Sometimes they run when they hear a motorcyle or bus go by ouside. They do learn eventually that certain noises are "safe". My roomie tends to rush about and usually slams the front door when he leaves (usually late) for work. The piggies have stopped getting startled by it.
I give my pigs time to get used to me when they are in the cage before I start taking them out of the cage. they are much less scared out of the cage when they know who you are and trust you.