Yep, I looked more closely and the substrate species is infected correctly most of the time, and this is the species that eventually takes over the substrate. But with two viruses and a variety of initial cell splits, the substrate looks pretty wild and crazy early on in the infection process.
I don't think theirs anything that special about the modes I used: it's primarily the relationship between the modes and how they copy over. Perhaps you can glean some hints from my previous post.
Post your own challenge to your fellow researchers!