Yesterday, I found the above website. I'm hearing more this year about caterpillars not making it through their pupation. Scroll down and look at C4.
"Diseases, Viruses, and Bacterial Infection
Monarchs are also suseptable to diseases, viruses and bacterial infection. Make sure you use dry paper towels when housing 3rd instar or larger caterpillars to help prevent fungal infections. Also, you may have to clean the larger caterpillars 2-3 times a day."