You may be overdoing the treatment. Try using black or chamomile tea to clean the eye very gently and then try leaving it alone. I once had a litter where some of the kits had nest-box eye and I worked very hard to cure it. No luck. I finally gave up and intended to cull the affected kits, but put it off for a couple of days. To my amazement, they began to improve when left alone. I concluded that my intervention after a certain point was only inflaming the eyelids.
Naturally you do not want to leave them with eyes stuck shut, but you could try going easy with the treatment for a day or two and see how they do.