The change over to a new tank often starts the system off into a new biological cycle. Have you been
closely monitoring your water quality through all of this? Have you been checking for ammonia, nitrites, pH, etc.?
Skimming v. non-skimming I would think should not affect the kinds of water quality issues related to flashing. Irritation of the gills from water quality issues are more or less related to ammonia and nitrite levels. A change-over or upgrade, would like contribute to water quality issues until the new tank settles.
I would not assume Marine Ich (
Cryptocaryon irritans) until I saw the spots. Make sure you inspect all your fish closely no less than twice a day.
I would not assume it
wasn't a disease, either. (Sorry

) For this case I'd seek out sources of contamination (new specimens coming in, equipment coming from another system, water coming in from an outside source, etc.).
I would be prepared to handle the situation as if it was a disease, in any case. Whether you quarantine fish or not, it is a good idea to have meds and/or equipment necessary to perform treatment.
I wish you luck! :rollface: