Yes, that's a good suggestion for the checkboxes.
At first I did this to prevent people from accidentaly make changes, but as you said, you have to click the save button anyway.
So I might remove them all, or least just leave one and only one, to enable edit mode.
About the dropdowns for favorite/visible, I won't change them for GUI consistency, and it's only a matter of one additional click, so you won't have an enormous gain of speed even if I put radio buttons instead...
About the amount of games = I think some words are missing in your sentence ^^ what do you mean ?
And finally, regarding your problem with the scraping function, this error is related to a network problem while attempting to connect to screenscraper. Your roms being stored on a NAS have nothing to do with this. It works like a charm at my office from my computer, and also at home where my roms are stored on my Pi.
Do you use a proxy or anything ?