I doubt anyone here has heard of scale rot. Your ig's skin problem could be caused by a burn.
Does he live with other iguanas? This could have been caused by an iguana bite.
What percent of his body is covered with the lesions? Is the lesion on his body, or on his tail?
Do the lesions bleed?
Is the cream an anti-fungal, or is it an antibiotic cream? Could it be Silvadene ointment?
Did your vet take a small sample of his skin to look for external parasites such as mites?