The tool just looks at notes from left to right.
Decoding the actual musical flow of a song would require many lines of error-prone code. NoteWorthy's flow rules are not completely documented and are a subject of some contention among users.
This aspect of the tool is unlikely to change unless there is widespread demand for it (with lots of data to test it against).
If you post an example clip of any staff that is causing a problem, I will look at it. I may be able to find a simple alteration to the clip or a program change that is less than a full flow decoder.
Glad that this has helped a bass player. I had hoped this to be of use for guitar, bowed string, and brass players who use a mute.
Edit: In this example, I added a tied grace note just before the repeat.!NoteWorthyComposerClip(2.0,Single)
|Clef|Type:Bass|OctaveShift:Octave Down
|Key|Signature:Bb,Eb,Ab
|Tempo|Tempo:170|Pos:11
|TimeSig|Signature:AllaBreve
|Bar|Style:LocalRepeatOpen
|Note|Dur:4th|Pos:3
|Note|Dur:8th|Pos:6|Opts:Stem=Down,Beam=First
|Note|Dur:8th|Pos:6x|Opts:Stem=Down,Beam=End
|Note|Dur:4th|Pos:6x
|Note|Dur:8th|Pos:2x|Opts:Stem=Up,Beam=First
|Note|Dur:8th|Pos:-4^|Opts:Stem=Up,Beam=End
|Bar
|Note|Dur:8th|Pos:-4
|Note|Dur:4th|Pos:n-2
|Note|Dur:8th|Pos:0^
|Note|Dur:8th|Pos:0|Opts:Stem=Down,Beam=First
|Note|Dur:8th|Pos:2x|Opts:Stem=Down,Beam
|Note|Dur:8th|Pos:0|Opts:Stem=Down,Beam
|Note|Dur:8th|Pos:2|Opts:Stem=Down,Beam=End
|Bar
|Note|Dur:4th|Pos:3
|Note|Dur:4th|Pos:n5
|Rest|Dur:8th
|Note|Dur:8th|Pos:6x
|Note|Dur:8th|Pos:2x|Opts:Stem=Up,Beam=First
|Note|Dur:8th|Pos:-4^|Opts:Stem=Up,Beam=End
|Bar
|Note|Dur:8th|Pos:-4
|Note|Dur:4th|Pos:-1
|Note|Dur:8th|Pos:1^
|Note|Dur:8th|Pos:1|Opts:Stem=Down,Beam=First
|Note|Dur:8th|Pos:2|Opts:Stem=Down,Beam
|Note|Dur:8th|Pos:1|Opts:Stem=Down,Beam
|Note|Dur:8th|Pos:2x|Opts:Stem=Down,Beam=End
|Note|Dur:4th,Grace|Pos:3^|Visibility:Never
|Bar|Style:LocalRepeatClose|Repeat:4
|Ending|Endings:7|Visibility:Never
|Instrument|Name:"[o]"|Patch:36|Trans:0|DynVel:10,30,45,60,75,92,108,127|Pos:10|Justify:Center|Placement:AtNextNote
|Dynamic|Style:f|Pos:-9|Justify:Right|Placement:AtNextNote|Visibility:Never
|Note|Dur:4th|Pos:0|Visibility:Never
|Bar|Visibility:Never
|Instrument|Name:"[x]"|Patch:115|Trans:-2|DynVel:10,30,45,60,75,45,108,127|Pos:10|Justify:Center|Placement:AtNextNote
|Dynamic|Style:f|Pos:-9|Justify:Right|Placement:AtNextNote|Visibility:Never
|Note|Dur:4th|Pos:0x|Visibility:Never
|Bar|Visibility:Never
|Instrument|Name:"[^]"|Patch:119|Trans:-2|DynVel:10,30,45,60,75,45,108,127|Pos:10|Justify:Center|Placement:AtNextNote
|Dynamic|Style:f|Pos:-9|Justify:Right|Placement:AtNextNote|Visibility:Never
|Note|Dur:4th|Pos:0X|Visibility:Never
|Bar|Visibility:Never
|Bar|Style:SectionClose
!NoteWorthyComposerClip-End
But strangely, NoteWorthy ignores the tie (except for the last time when it creates a hanging tie). I'll stop short of calling this a bug since by design, grace notes are not fully implemented.
This might be a better option:!NoteWorthyComposerClip(2.0,Single)
|Clef|Type:Bass|OctaveShift:Octave Down
|Key|Signature:Bb,Eb,Ab
|Tempo|Tempo:170|Pos:11
|TimeSig|Signature:AllaBreve
|Bar|Style:LocalRepeatOpen
|Instrument|Name:"Slap Bass 1"|Patch:36|Trans:0|DynVel:10,30,45,60,75,92,108,127|Pos:16|Placement:AtNextNote
|Dynamic|Style:f|Pos:-9|Justify:Right|Placement:AtNextNote|Visibility:Never
|Note|Dur:4th|Pos:3
|Note|Dur:8th|Pos:6|Opts:Stem=Down,Beam=First
|Note|Dur:8th|Pos:6x|Opts:Stem=Down,Beam=End
|Note|Dur:4th|Pos:6x
|Note|Dur:8th|Pos:2x|Opts:Stem=Up,Beam=First
|Note|Dur:8th|Pos:-4^|Opts:Stem=Up,Beam=End
|Bar
|Note|Dur:8th|Pos:-4
|Note|Dur:4th|Pos:n-2
|Note|Dur:8th|Pos:0^
|Note|Dur:8th|Pos:0|Opts:Stem=Down,Beam=First
|Note|Dur:8th|Pos:2x|Opts:Stem=Down,Beam
|Note|Dur:8th|Pos:0|Opts:Stem=Down,Beam
|Note|Dur:8th|Pos:2|Opts:Stem=Down,Beam=End
|Bar
|Note|Dur:4th|Pos:3
|Note|Dur:4th|Pos:n5
|Rest|Dur:8th
|Note|Dur:8th|Pos:6x
|Note|Dur:8th|Pos:2x|Opts:Stem=Up,Beam=First
|Note|Dur:8th|Pos:-4^|Opts:Stem=Up,Beam=End
|Bar
|Note|Dur:8th|Pos:-4
|Note|Dur:4th|Pos:-1
|Note|Dur:8th|Pos:1^
|Note|Dur:8th|Pos:1|Opts:Stem=Down,Beam=First
|Note|Dur:8th|Pos:2|Opts:Stem=Down,Beam
|Note|Dur:8th|Pos:1|Opts:Stem=Down,Beam
|Note|Dur:8th|Pos:2x|Opts:Stem=Down,Beam=End
|Bar|Style:LocalRepeatClose|Repeat:4
|Ending|Endings:7|Visibility:Never
|Instrument|Name:"[o]"|Patch:36|Trans:0|DynVel:10,30,45,60,75,92,108,127|Pos:10|Justify:Center|Placement:AtNextNote
|Dynamic|Style:f|Pos:-9|Justify:Right|Placement:AtNextNote|Visibility:Never
|Note|Dur:4th|Pos:0|Visibility:Never
|Bar|Visibility:Never
|Instrument|Name:"[x]"|Patch:115|Trans:-2|DynVel:10,30,45,60,75,45,108,127|Pos:10|Justify:Center|Placement:AtNextNote
|Dynamic|Style:f|Pos:-9|Justify:Right|Placement:AtNextNote|Visibility:Never
|Note|Dur:4th|Pos:0x|Visibility:Never
|Bar|Visibility:Never
|Instrument|Name:"[^]"|Patch:119|Trans:-2|DynVel:10,30,45,60,75,45,108,127|Pos:10|Justify:Center|Placement:AtNextNote
|Dynamic|Style:f|Pos:-9|Justify:Right|Placement:AtNextNote|Visibility:Never
|Note|Dur:4th|Pos:0X|Visibility:Never
|Bar|Visibility:Never
|Bar|Style:SectionClose
!NoteWorthyComposerClip-End