This is undoubtedly because ScreenScraper requires the hash of the files. It take a looong time to hash those PSX files. Nothing that can be done about that. Luckily Skyscraper has a system I dubbed QuickId which saves the hashes and only rehashes when the file has changed on the disk. So for any game list regeneration it will be fast. But the first time any file is hashed, it will have to calculate it from the data inside the file.
EDIT: I spoke too quickly... My QuickId system is only used for the internal Skyscraper ID's... I should fix that, but I'm not actively developing Skyscraper right now, so you will have to live with it for PSX for the time being I'm afraid.
Optimally the Skyscraper internal ID's should use hashes. But i limited it to only hash files when they are smaller than 50 megs I think (because it would take too long for bigger files, which is also the issue here). So for anything above that, it simply hashes the filename. And it's one of those things where it could easily be made to always use hashes for the full files, but then I would break the caches of every single Skyscraper user. Can't do that... Ugh. I really should have given those ID's more thought back when I designed it two years ago. Keeps coming back to kick me in the behind. :(