Some multi-page online articles don't offer a 'print' view or 'single-page' view, so each page has to be separately marked using Instapaper (example article:
http://www.thestreet.com/story/10226...recasting.html). If you do this in sequence, Instapaper stores the articles such that the last page is newest, and the first page is oldest. When fetching the Instapaper recipe in Calibre, the ebook created will use the same sequence, so the book starts with the last page of the article and ends with the first page.
An obvious, but not particularly elegant, workaround is to mark the article pages in reverse order.