I often had this problem with InDesign CS3 (and I think CS2 also).
When composing a paragraph in InDesign, the last line will often be further away,
is that a known issue about InDesign. I checked the paragraph option (space afters, space befores, etc) and there is nothing: All line in the paragraph have the same characteristics.
There are no characters in subscript or superscript mode.
Louis, are you using fixed leading or autoleading? If you're using autoleading, any variation in point size on a line of type will affect the leading above that line. It's usually caused by a carriage return in a different point size on the terminal line of a paragraph, often in copy imported from Word.
Addendum: So far as I'm aware, InDesign contains all-new code, with nothing carried over from PageMaker. I'm sure Dov Isaacs will come along to confirm this for us.
Be sure there is a hard return after last paragraph. I get a lot of word files with no hard return after the last paragraph in a section/chapter and when I place into ID, the last line floats away until I enter a hard return.
A lone paragraph return at the end of a story will never cause overset, but if you have an XML-closing-tag after that paragraph return (or any white space character), then you'll get an overset warning even though the only overset item is non-printable and not relevant to most of the things that one worries about for overset text.