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Toxaris -
Item 1 happens very occasionally, but I haven't seen it in most recent releases. When it does happens I am, by definition, at a point where stop/start Word isn't a big deal.
Item 3 - never bothered me, I only reported now for 'the record'.
Item 2 - all I really want to know is
some or
no words were marked. If some were marked I don't much care if it was 2 or a 102. What I do care about is if it reports 5 and my search for
^? Highlight finds none. The search is in a macro with a kbshort, so it's not a case of me mis-keying it.
I can do some testing if you need it - my 'apprentice' is doing what I thought I'd be doing this month

My intuition is still that 1 & 3 may have the same underlying cause - something is storing something where it shouldn't - used to known as a 'scribbling'.
Request : at the end of Marking could you clear the Replace With Highlight Option - maybe best to clear everything. The eye balling of the highlighted words, sometimes triggers me doing a replace all. If I forget to clear it then the Highlight carries over into my replace...

on file selection in Mark - used it a few times today,
much easier than selecting the file in Settings every time.
BR