Tom,
Not sure you understood me entirely. We were copying and pasting the text into TextEdit in order to remove any previous styling, notes and non-text characters. Then pasting that text from Text Edit back into the same original text box InDesign.
So we weren't making any new text boxes, or recreating assignments. So far, thats been working for fixing the errors.
We've told our offsite vendors to try changing how they import their text from the Word manuscript. When they place type, they must now click on Show Options and then select Remove Styles and Formatting from Text and Tables. When we get the next round of files back, we'll know if that did the trick or not.
And I agree entirely with you and Chad. This back-and-forth with you is helpful if only to give Adobe direction in resolving the issue. It may need either an application change, or just some greater understanding on our part, but the exact problem still remains unclear.