I also have a similar problem, using Acrobat Standard 9, and Windows 7.
A file printed to pdf from another application looks fine in Acrobat. When I add a note using either the typewriter tool, or the textbox tool, the characters are wrong. I can see that the characters are all displaced by the same number of places relative to the keyboard, eg you type "qwerty" but it comes out as "asdfg". I'm still looking in the forums and on google for a solution.