What would be the cause of the history of pond only developing the problem a few years ago? I wouldn't think the soil is much different than before. It might be good to explore this line of thought. Early on, was there a treatment that affected water chemistry? One thought, maybe it lost its earlier alkalinity over the years and the recent liming will help ... given time. Another thought, maybe mechanical disturbance is worse than thought, eg maybe other species that OP isn't aware of? Yet this wouldn't explain two weeks and a jar not settling.

Anyways, good luck and keep us posted about progress.

It isn't what we don't know that gives us trouble, it's what we know that ain't so - Will Rogers