Pagination suffix & reuse_query_string problem

No, that bit is not the right place to look. That is for a standard segment url. It is the first clause of the above "if" is where your string is being generated (I think! Not an expert).

Above that is the clause that applies with the query string, and I cannot see where the suffix is added. I gave up after that point as I thought it was a long shot anyway, and because I thought someone else might have an input on it for you that knows better than me. If you look later it removes and then re-adds the query string in a most peculiar manner.