Are you looking the Channels area or the EPG? Just wondering, I think channel logos in the EPG are a separate thing. I only see channel logos in "Channels" and for things like the Recently Played tiles. In the EPG I only see the channel numbers and names; I think this is the default behavior.I've tried to clear the data. Same result. No channel logo's in Kodi from the HDHomerun backend. You mention giving Kodi the URL's? How do you do that?
As for the URLs, SiliconDust provides them as part of the guide data. When you give Kodi the channel list it gives you a way to specify the URL of the channel logo; same for the program thumbnail you see in the EPG. All the PVR client has to do is pass that information on, the magic as it were all takes place in Kodi.
If you see channel logos anywhere, then the data from SiliconDust is good. If you don't get them anywhere at all, perhaps they are missing in the guide data. We can walk through checking that if you'd like, it involves a few steps and some copy/pasting, but it's not too terrible.