OK it took a bit to figure it out but I had a couple of games that extracted into sub folders. Those sub folders were what was crashing the scraper. Once I fixed that the scraper started functioning correctly again.
@jailer
And where in the settings? I have the same problem. I wonder why people always write that the problem is solved, but not where they found it to help other.
Is it so hard to find ?
Main Menu -> Advanced Settings -> Advanced Emulator Configuration
Chose the System you want and you can change Emulator & Core for all Games !