[DeArmin]

That's how it's supposed to work. The text editor is showing you the contents of the file itself and letting you edit that. The transpose dialog is just transposing whatever chords are present in the file. If you want the transpose to actually modify the file, use the transpose feature in the text editor itself, not outside the text editor. Then the file will be modified and all the chords will be changed. 

Mike

I think we have a misundestanding. Only the chords in the verse and chorus were transposed, not in the Intro. I think there is a problem with the "separators". See the new file which i have attached.
  MS Transposing.pdf (Size: 239.41 KB / Downloads: 8)