Hey, I was having the same exact issue, basically the same point it started failing too, after I applied the BannerBox theme.
I went through all the steps besides copying over my data, because I have quite a bit of games in the collection. But, found one thing: I installed a fresh version of LaunchBox and went to that Launchbox/Core folder and saw that there were symlinks set up, but for some reason the sym links on my broken version aren't linked to those folders any more. LaunchBox will create the folder, but it just isn't linked to the actual theme folder anymore.
Update:
After moving all of my data (Data, Images, Manuals, Metadata, Music, Videos) over to the new directory of the fresh LaunchBox install, everything seems to work fine. For what ever reason the symlinks that are in the Core folder all broke sometime after installing the CoverBox theme... weird.