Courtesy Accidental errors when opening 0.9.5 files with 0.9.6.1 version

Now some problems where solved in 0.9.6.1 version, but one still remains and I think to have detected the cause.
In practice, opening a 0.9.5 file in 0.9.6.1 causes the program to add courtesy accidentals everywhere...
I write small pieces or organ exercices that last less than one page and make files of two or three pages. In version 0.9.5 a piece with no accidentals was suited by one with five sharps and then by one with no accidentals again with no problem.
Opening it in version 0.9.6.1 the piece preceding that with five sharps shows five naturals after the clefs in all lines for the entire piece. The piece that follows shows five naturals on the first line only (but I do not need it and 0.9.5 works correctly in this respect). I noted that 0.9.6.1 has in the STYLE>Modify Style>Page panel the new option "Courtesy accidentals" that is lacking in 0.9.5.
Nevertheless, even unchecking this option and saving the file as 0.9.6.1 the problem persists when the file is reopened.
As I have many pages full of these small pieces with varying clef accidentals I was forced for the moment to revert to 0.9.5 version because the resulting layout is a real mess: sorry!
Thank you for your help!

Mac OS 10.4.11 Tiger.