Bubbles in the eyes are a definite sign of CRD. If the current antibiotics aren't working that's a pretty sure bet. Go to your local farm supply store and buy a bottle of Tylan 50 injectable and a small gauge needle like a 100 unit/1ml insulin needle. Give 1 cc in each chicken's breast muscle daily for 3 days.
How you administer the shot:
Draw up your injection prior to getting a hold of the chicken, as the medication is thick especially if it has been refrigerated and can take a while to draw out. Pull back the plunger on your needle and inject the vial with a full syringe of air. Flip the vial upside down and pull back the plunger to draw out the medication. It will fill the syringe slowly and this is normal. Have someone else hold the bird so you have access to the breast. You can do it by yourself by holding the bird's back to your chest to expose the breast. Make sure the bird is held securely so it doesn't kick or flap around. Feel for the breast bone or keel that runs down the center of the chicken's chest/belly. Pull back the feathers to reveal the skin and inject the needle at a 30-45 degree angle, a 1/2 inch or so away from the bone. Do not inject any deeper than 1/2 to 3/4 of an inch or so, most insulin needles aren't any longer than that anyway. Inject parallel to the breast bone. Treat with 1ml (equivalent to 100 units in an insulin needle) for 3-5 days but no longer. If you have several chickens to treat, it is good practice to fill the number of syringes you need with medication before you begin.
We just treated a Speckled Sussex rooster I bought to breed to our SS hens and I didn't notice he had any rattling and eye bubbles til after we got him home. We treated him with Tylan and now he is perfect. The symptoms went completely away. I swear by Tylan.. it is a staple at our house for CRD and is kept on hand at all times.