The last few batches my wort is going from crystal clear before whirlpool, which is also going through a plate chiller, to cloudy after the fact.
I have a 3 vessel, single tier system. I recirculate for the entire mash, so the wort going into the boil kettle is extremely clear. After a 60 minute boil, the wort is still really clear, with a bunch of large protein clumps starting to form and fall down to the bottom. This is when I run the wort through a plate chiller and whirlpool it. If I'm adding a bunch of hops, I won't chill it down right away. If I'm not, then I chill it down right away. I always recirculate it back into the kettle and chill it down. The plate chiller gets it down to 50-75f in 10-15 minutes, depending on ground water temp.
The past few brews, the wort is going into the plate chiller clear, then coming out cloudy. I'm not sure if the large protein clumps are getting sucked into the plate chiller, breaking up while passing through and coming out as small particles. Or if the force of the whirlpool is breaking up the protein clumps while it's whirlpooling inside the kettle. I'm thinking it's the first option, since I've played around with the flow from the pump and it doesn't seem to matter.
I've also done this same exact setup and the wort remained clear, with the large protein clumps remaining. I'm not sure what would have changed? I baked my plate chiller in the oven recently for a couple of hours and flushed it out good. I figured that would help it, not hurt it.
I use a mesh bag for all my kettle additions, so nothing is getting sucked into the plate chiller, other the wort.