It does sound like possible mycoplasma gallisepticum (MG.) It can cause the bubbles in the eyes as well as other respiratory symptoms. Symptoms can come back during periods of stress, and it is contagious to other chickens. Tylosin powder in the water, or Tylan injectable given orally 025 ml per pound 3 times a day for 3-5 days can be a good treatment. Some use oxytetracycline. The LA 200 is injectable and given once a 3 days. Most people would close their flocks with MG. It can pass through hatching eggs.