Hi!
1. What types of results are the images missing on? Are these posts/products or any other post type, or maybe attachments or categories? Let me know, I will check the source for differences.
2. I am not sure if I am able to tell, but it I am almost certain it is the custom field filters, if nothing else differs. Try removing the custom field filter to see if it makes any difference. If so, then either the filter values or something around there is the problem.