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I always found that constantly talking to my 6 piggies helped a lot with their skittish-ness (if that's even a word lol). When they were younger i used to spend hours just sitting next to their cages and talking to them. Eventually they would venture out while i was sitting there - sometimes i would hold a piece of veg and they would come a sniff it (i would hold my hand real still and not make any sudden movements) eventually they would take the food from me and run. In time they would come to the side of the cage for food.
I also associated their veg with the words 'yum, yums' and whenever i had some tasty treats i would call out the words 'yum, yums' and rustle a bag - every time they noe hear a bag rustling they think of good things and scream at the top of their lungs till you bring them some.
Lap time is a good way of them getting used to you. I always made sure i had a piece of lettuce, red pepper, or carrot with me - guinea pigs love food - so they instantly see us as the people with 'yum, yums' - how can a guinea pig resist? I kept lap time to a minimum (say 5-10mins of cuddle time) - and only have them out for maybe 10-15mins now (and my two youngest are 7months old now).
3 of my 6 guinea pigs will happily sit there and allow you to pick them up while the other 3 it's a bit of hide and seek when it comes to lap time (funnily enough the three that give me the run-around are the 3 less dominant piggies of my pairings). One of my boys is still quite skittish and any sudden movements have him running and hiding - so believe me it's nothing you are doing - some guinea pigs are skittish by nature and some never get rid of it completely. My shy boy (as we call him) doesn't crave attention (well not human kind anyhow) and i don't think is really motivated by food (well he may kill for a piece of parsley) - so we don't push him and we make sure we are extra quiet when he's out when we approach the cage.
Give them time and i'm sure they'll come out of their shell's. Do you have an indoor run or area they can come out and run around in safely? I found this helped a alot with my first boy - within two weeks of us having him he was happily being handled, coming to the side of the cage for food and even coming to us when we called his name (mind you he is what we call our human guinea pig lol)
Sorry about the long winded post - just wanted to give you some idea of what helped for me - do they have lots of toys to play with in their cage? loo rolls with a slit cut down the middle filled with hay make a great toy and piggies go crazy for them!
any ideas on how to calm them down? Any thoughts at all would be appreciated! x
