You put 5 Guineas out, but the flock only accepted 3 of them? Are you positive the 2 they are running off are Hens, or are they males?
Guineas need to be acclimated to each other gradually to be succesfully integrated... established, territorial flocks don't usually instantly accept new additions right away (especially while it's still breeding/laying season). Housing them side by side but separated by wire for anywhere from a couple wks up to six wks or more so they gradually get used to each other is what usually works best for most people when they are integrating new birds into their flocks.
Since your older flock is already free ranging then if you have a large wire dog crate that you can put the 2 other birds in and then keep them in that out in the area that all the older birds free range that should help them get used to seeing each other (and the other birds will not be able to run them off). You will want to bring the crate into the safety/shelter of the coop each night tho.
Once the weather cools down and the daylight hours shorten my flocks all settle down and there is less aggression. And that may be when your flock finally accepts the 2 birds (that is if those 2 live that long and don't get taken by a predator before then).
