I fed some wet rye that had been wrapped last year. It worked fine until we had a warm up around the first of March then I noticed a white mold on it throughout the bale....like you I had seen worse and fed worse. Within a week to 10 days I had 2 cows come down with it....one that had already calved and one still with a calf in her....had to shoot them both. Then about a week after I stopped feeding the rye a 3rd one comes down with it and the vet said I could not give her enough penicillen and oxytetrcyclin to save her but I was able to prove him wrong after 2 weeks of very high doses of both. It's some bad stuff. I hope that you can save them. I would  recommend to either quit feeding it altoghether or if you have capabilities to mix it with better quality roughage. My personal opinion is mixing is the key as it spreads it out more uniformly and lowers the concentration. Needless to say I didn't put any rye out this past year. Good luck!