Kevin, after reviewing your files, I can see that the cause of the problem is the use of special endings with local repeats. Special endings should only be paired up with Master Repeats. Local repeats do not use special endings.
So, your bar 12 and 13 should look like this:
!NoteWorthyComposerClip(2.0,Single)
|Bar|Visibility:Always
|Ending|Endings:1|Visibility:Always
|Note|Dur:Half,Dotted|Pos:-4|Opts:Stem=Up,Slur=Upward,ArticulationsOnStem
|Text|Text:"Repeat poco più %"|Font:StaffItalic|Pos:-13|Justify:Right|Placement:AtNextNote
|Note|Dur:4th|Pos:-4|Opts:Stem=Up,Slur=Upward,ArticulationsOnStem
|Bar|Style:MasterRepeatClose
|Ending|Endings:2|Visibility:Always
|Note|Dur:Half,Dotted|Pos:-4|Opts:Stem=Up,Slur=Upward,ArticulationsOnStem|Visibility:Always
|Note|Dur:4th|Pos:-4|Opts:Stem=Up,Slur=Upward,ArticulationsOnStem
|Bar
!NoteWorthyComposerClip-End
This will also solve your issue of the local repeat count showing up on the bar.