No its not normal. There were a few recent threads about cloudy maxibloom reserviors, and at least one ended up being nasty bacteria hiding in the RO filters on the input end that had to be replaced before it stopped. Like you said, there are some pathogens that pool shock won't even touch, and will keep replicating anyway..
I think you have too many pumps by sharing one res between that many systems. I counted like 4-5 at least when you showed the picture of your res. Its the flower one your having problems with, right? I think I rmember you say the veg res is always clear, and the plants grow fine, but the flower one is really cloudy with lots of residues, and all the plants fed from it keep having problems.
When you have that many pumps dangling down into one res, it heats up more, and has way more surface area and nooks and crannies for the pathogens to colonize.
MAybe you would be better off to use dedicated reserviors for each setup. At least if one res goes bad/cloudy, you won't be contaminating all the plants at the same time.. If that's even the case..