It seems the problem is about soft hyphenation.
The paragraphs that have changed are only the paragraphs with soft hyphenation.
Looks like myTextFrame.duplicate() does not keep this information.
Perhaps TextWrap may interfere in this case. For example when we duplicate a text-frame which has some TextWrap. Here is an attempt to solve this problem:
Thanks for your answer, unfortunately your script did not solve, it just does the same.
Just an idea: is it possible this is a document created in an earlier version of InDesign, and the duplication triggers a recomposition that behaves a little differently in CS5?
To test this, try recomposing the story in the original and see if it changes. (Hit Command-Option-/ or Ctrl-Alt-/ to recompose all stories.)
Yes the document has been created in Indesign CS4, but I have no more ID CS4 to make the test you suggested.
But it seems you are right, the composition behaves a little differently in CS5 : while the text stay correctly hyphenated on opening in ID CS5 (I mean hyphenated as in ID CS4), hyphenation changes after a recompose all stories command.
Sorry to answer so late... Thanks for your help.