It sounds like manually scrapping each or manually resizing each (out side es-scrapper – using photoshop or paint) is viable, but this is a maintained project so there should be a fix at some point sooner than later.
I plan to just sit tight and wait for the author to check out the problem (it might not hurt to reach out to him via git and let him know there is a issue – he may not be aware). I took this opportunity to clean up my roms and copy of a fresh list. I’m going to keep an eye on the git page and watch for an update. If I don’t see a new release in the next few weeks, I’ll go the manual route.