Looks like that has done the trick Tom - thank you SO MUCH mate. I think I may have corrupted the database or something by changing the folder locations of the library (I moved them into folders by Publisher) whilst Ubooquity was scanning the library at the same time :/ by removing the old database, it has scanned the 3000 comics, but this time they show up in the total and thru the web interface - Thanks again Tom, you're a god among men I swear!

Update: I updated Java.

I also watched a scan of the library complete. It reports that it added/updated 2990 comics, removed none and total comics = 0.

Change: When I load Ubooquity in my browser, I now get comics listed, but the thumbnails are either the generic folder icon, or the same cover repeated for all thumbnails.

While I can navigate through to the 'Read/Download' option, after I make a choice, the comic tries to load, the timer craps out and I get a Page Not Found error.