Frustrated Chick owner..

[rancher hicks]

Sorry I didn't get to this sooner, I use wood chips. Straw in the nest boxes. I take out a little of the yukiest stuff and add some more to keep things as clean w/o doing a whole cleanout.

 

[farmin'chick]

I'm sure you know lots about chicks, but the things I would check for that problem are:

Dry, clean bedding
No exposure to spilled feed
If there is spilled feed that becomes damp, it can mold or attract flies, and the flies that eat spoiled wet feed lay eggs that turn into maggots that can carry botulism, which little critters unfortunately the chicks like to eat
The brooder has been cleaned and disinfected before use -- preferably sterilized, or fresh painted
No draft
Enough warmth so that the chicks don't pile up at night
The chicks should always stay dry. If I have a bunch of water spillers, I will use what I call a "duck box" -- a shallow box with screen wire on the top to set their water on, so they can't spill it and wet their bedding
Reduce dustiness

An old timer's remedy for Roup, which is pulmonary wheezing, is to give molasses in warm water.

 

[rancher hicks]

the best advice for chicks and brooding is a good book. I checked out every book on chickens I could get my hands on at the public library. If you don't have one might I suggest starting one. I am sure there are plenty of folks who would donate books to it.
reading up on chickens is the "FIRST" thing you should do before getting chicks or chickens. The second make sure you are prepared for them before you get them. The third join this site. The fourth subscribe to "backyard poultry magazine".