Wahou! I have never seen such a lively dashboard! So many icons, so many colors! :)
But anyways, YOU ARE RIGHT. I can see it clearly here, the files are all missing, and the plugin cannot detect any of them. You are using only the "zombie" sizes, right?
There are two bugs on my side. First it displays the "clock" icon, but actually the plugin should be already aware that there is an issue and shows something else (something like a skull, haha) to avoid any miscomprehension. Then there is the bug related to the fact that it cannot find the real path to the file. And as you said, it's probably linked to the network WordPress.
That's not going to be very hard to resolve, but I think I will need a bit of your help. Do you mind contacting me by email? http://www.totorotimes.com/about. We'll work on it together (should be fast), then I will release a new version on Monday including the fix. Thanks a lot :)