Alan, I think you are probably right. Except that the new trees, out in the orchard did not get any mulch right away. And when they did, I used a different mulch. Cypress instead of hardwood chips. And we tried the cardboard - which kept weeds down, but needed constant tinkering. So, I ordered a load of cypress mulch and we put it on top of the existing cardboard.
I’m beginning to think that the fungus came in with the mulch (like you said) - or with the trees I bought. Until I get an irrigation system set up for the poms in the field, I am afraid to leave them un-mulched. We had a long hot dry spell that scared me. So, I was pulling hoses all over the field and moving them all of the time.
I considered taking up all of the mulch and putting down large squares of landscape fabric. But, something needs to go on top of that - or weeds will grow under it. And who knows . . . maybe the fungus will grow underneath, too.
I am trying to recall if my first pomegranate tree ever had fungal problems before I planted the Granada. ? I don’t think it did. I had a couple of years with clear fruit.
This year is the worst. I have been spraying the fruit and unopened buds with Captan, as the IFAS literature recommended. For next year - I am considering ordering a bottle of that expensive fungicide that worked in their field trials in FL. (Cabrio or LunaExperience) It would be worth it, if it will control this fungal problem . . . even somewhat.
Captan was recommended for the fruit, but Mancozeb for the foliage.
I plan on spraying the heck out of them when they are dormant. The ground as well.
I don’t know what else I can do.