As you observed, when you have two consecutive arpeggios which have the same notes, and the second arpeggio is anticipated, some of the "note on" events for arpeggio #2 are inserted before the corresponding "note off" event for arpeggio #1. Sort of like the following picture, where 1 represents a "note on", and 0 represents a "note off":
1 0|1 0
1 10| 0
1 1 0| 0
1 1 0| 0
The net result is that the "note off" events for the 2nd arpeggio are making the 1st arpeggio notes end early for all but the top (final) note, so that note "sticks out".
I can't think of an easy way to fix this. As has been noted previously, anticipated arpeggios (and guitar chords) are sort of primitive time travel devices, since they place MIDI events in the past, relative to the location of the object. In the above example, I guess what you are hearing is the result of the causality violation that I refer to in the documentation
One workaround to get normal playback would be to create a second layered staff and alternate the like chords between the two staves, making sure to use a different MIDI channel for each staff. Something like this:
!NoteWorthyComposer(2.751)
|AddStaff|Name:"Staff"|Group:"Standard"
|StaffProperties|EndingBar:Section Close|Visible:Y|BoundaryTop:12|BoundaryBottom:12|Lines:5|WithNextStaff:Layer|Color:Default
|StaffProperties|Muted:N|Volume:127|StereoPan:64|Device:0|Channel:1
|StaffInstrument|Trans:0|DynVel:10,30,45,60,75,92,108,127
|Clef|Type:Treble
|Key|Signature:Bb|Tonic:F
|TimeSig|Signature:4/4
|Rest|Dur:4th|Opts:Stem=Up
|Bar
|User|Arpeggio.ms|Pos:-3|Anticipated:Y
|Chord|Dur:Whole|Pos:-6,-3,-1,1,4|Opts:Muted
|Bar
|Rest|Dur:Whole|Visibility:Never
|Bar
|User|Arpeggio.ms|Pos:-3|Offset:0|Anticipated:Y
|Chord|Dur:Whole|Pos:-6,-3,-1,1,4|Opts:Muted
|Bar
|User|Arpeggio.ms|Pos:-3|Offset:0|Anticipated:Y
|Chord|Dur:Whole|Pos:-7,-5,-3,0,2|Opts:Muted
|Bar
|User|Arpeggio.ms|Pos:-3|Offset:0|Anticipated:Y
|Chord|Dur:Whole|Pos:-6,-3,-1,1,4|Opts:Muted
|Bar
|Rest|Dur:Whole|Visibility:Never
|AddStaff|Name:"Staff-1"|Group:"Standard"
|StaffProperties|EndingBar:Section Close|Visible:Y|BoundaryTop:10|BoundaryBottom:10|Lines:5|Color:Default
|StaffProperties|Muted:N|Volume:127|StereoPan:64|Device:0|Channel:2
|StaffInstrument|Trans:0|DynVel:10,30,45,60,75,92,108,127
|Clef|Type:Treble
|Key|Signature:Bb|Tonic:F
|TimeSig|Signature:4/4
|Rest|Dur:4th|Opts:Stem=Up
|Bar
|Rest|Dur:Whole|Visibility:Never
|Bar
|User|Arpeggio.ms|Pos:-3|Offset:0|Anticipated:Y
|Chord|Dur:Whole|Pos:-6,-3,-1,1,4|Opts:Muted
|Bar
|Rest|Dur:Whole|Visibility:Never
|Bar
|Rest|Dur:Whole|Visibility:Never
|Bar
|Rest|Dur:Whole|Visibility:Never
|Bar
|User|Arpeggio.ms|Pos:-3|Offset:0|Anticipated:Y
|Chord|Dur:Whole|Pos:-6,-3,-1,1,4|Opts:Muted
!NoteWorthyComposer-End