Yes, i have run into several problems with your plugins on my multisite where things don't work. I am thinking however it might be permissions. I also added a six and 7th site and when i try to login to them it says that cookies are not enabled but they are. I have seen this error before. also i tried to upload files from a migration through SSH but it would not allow me to do it.
I also want to know if one of your plugins can be used to migrate a single install site to my new multisite install.