Rust bacteria are not, I believe, orange. In any case, persist as orange sediment in a chlorinated pool. Please understand that iron tests (a) are often inaccurate and (b) ONLY measure dissolved iron. By definition, orange sediment on the bottom of your pool is no longer dissolved.

I am getting the impression you have never bucket tested your well water BEFORE it went through any filter or softener. Is that correct?

Also, it's typical that wells with iron contaminated water vary from time to time and season to season with respect to how much iron is present in the water.

Regarding filling -- using the polyquat and HEDP AS YOU fill, followed by trichlor tabs in the skimmer, is intended to (1) kept dissolved iron dissolve for awhile (HEDP), (2) help clump and filter the iron as it changes from soluble to insoluble forms (polyquat), (3) allow you to remain algae free while maintaining relatively low chlorine levels (polyquat), and (4) 'push' the iron to make the change from soluble to insoluble, just upstream of the filter (trichlor tabs in the skimmer).