Have you tried formalin dips?
I'm dealing with something similar, but not exactly the same. I think I did have an original fluke issue, but with repeated treatments the issue did not completely resolve. Now I'm seeing what I guess are a few ich spots here and there, along with opaque/cloudy blotches, which I originally thought were skin flukes until nothing came off in a FW dip.
Now I'm doing TTM on all the fish to eliminate ich as a possibility. Also doing formalin dips and antibiotic (NFG) during the course of TTM. Maybe it's just because I'm paying more attention, but I think theres something nasty circulating in the hobby... seeing a lot of reports of flukes, prazi-resistant flukes, and unknown issues.