i think maybe you need to change nutes. your hydroponic (am I correct?) nutrients are lowering the pH as you said yourself, but I think not all fertilizers do that (not sure though. but I think biobizz for instance doesn't). IF you are in soil you might want to use organic fertilizers. I'll bet your water is very soft too, which is why it's so sensitive on the pH (going down so drastically with the nutes). your pH that's off is probably the reason for your different problems, it may be aggravated by high salinity but I guess flushing doesn't help in such a case (so we learn anyway).
So another method you could *try* to overcome this is to add just calcium to your nutrient solution. You can try getting those pharm tablets they sell as an additive for humans, i think that should be good to use, or just some boil some eggs in your water (haven't actually tried any of those). perhaps calmag could be an answer too, but I think maybe the magnesium will undo the calcium effect - calcium buffers your water up, this is why hard water (which contain a lot of calmag) is less sensitive on pH.
good luck and tell us how you do.