Those pictures are so cute, sorry the chicks have to be in fear of their lives to get them.
On a serious note about photography though. on camera flash is probably about as poor a choice as you can go with to get really good pictures. a light tent with defused light would render much better detail and color saturation. I don't have the time at the moment to go into detail about it but do a little searching on photographing things like jewelry. a tent can be made from anything that will make a frame and covered with cloth or even copier paper. just keep in mind you need very strong light because it has to pass through that cloth or paper, think along the lines of 2 500 watt lights.
You can also specifically search for Macro Photography which is actually what you are trying to attempt when getting pictures of chicks. A camera that has a macro ability is also very helpful.
you also avid the flash startling the chicks because the lights are constantly on.