I am looking forward to your example. I tried to recreate what you were describing, and I am not seeing the problem you describe. But maybe my example is too simple a case.
Just out of curiosity, what version of NWC are you using? (I tried this in both 2.51a and in the current beta version of 2.75, with identical results.)
!NoteWorthyComposer(2.51)
|Locale|ACP:1252
|Editor|ActiveStaff:2|CaretIndex:9|CaretPos:-2
|SongInfo|Title:""|Author:"<Name>"|Lyricist:""|Copyright1:"Copyright © 2015 <Name>"|Copyright2:"All Rights Reserved"
|PgSetup|StaffSize:16|Zoom:4|TitlePage:Y|JustifyVertically:Y|PrintSystemSepMark:N|ExtendLastSystem:N|DurationPadding:Y|PageNumbers:0|StaffLabels:None|BarNumbers:None|StartingBar:1
|Font|Style:StaffItalic|Typeface:"Times New Roman"|Size:10|Bold:Y|Italic:Y|CharSet:0
|Font|Style:StaffBold|Typeface:"Times New Roman"|Size:8|Bold:Y|Italic:N|CharSet:0
|Font|Style:StaffLyric|Typeface:"Times New Roman"|Size:7|Bold:N|Italic:N|CharSet:0
|Font|Style:PageTitleText|Typeface:"Times New Roman"|Size:24|Bold:Y|Italic:N|CharSet:0
|Font|Style:PageText|Typeface:"Times New Roman"|Size:12|Bold:N|Italic:N|CharSet:0
|Font|Style:PageSmallText|Typeface:"Times New Roman"|Size:8|Bold:N|Italic:N|CharSet:0
|Font|Style:User1|Typeface:"Times New Roman"|Size:8|Bold:N|Italic:N|CharSet:0
|Font|Style:User2|Typeface:"Times New Roman"|Size:8|Bold:N|Italic:N|CharSet:0
|Font|Style:User3|Typeface:"Times New Roman"|Size:8|Bold:N|Italic:N|CharSet:0
|Font|Style:User4|Typeface:"Times New Roman"|Size:8|Bold:N|Italic:N|CharSet:0
|Font|Style:User5|Typeface:"Times New Roman"|Size:8|Bold:N|Italic:N|CharSet:0
|Font|Style:User6|Typeface:"Times New Roman"|Size:8|Bold:N|Italic:N|CharSet:0
|PgMargins|Left:1.27|Top:1.27|Right:1.27|Bottom:1.27|Mirror:N
|AddStaff|Name:"Staff"|Group:"Standard"
|StaffProperties|EndingBar:Section Close|Visible:Y|BoundaryTop:12|BoundaryBottom:16|Lines:5|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
|Lyrics|Placement:Bottom|Align:Standard Rules|Offset:0
|Lyric1|Text:"These are lyr-ics\r\nand so are these.\r\n"
|Clef|Type:Treble
|TimeSig|Signature:4/4
|Note|Dur:4th|Pos:1
|Note|Dur:4th|Pos:0
|Note|Dur:4th|Pos:-1
|Note|Dur:4th|Pos:-2
|Bar
|Ending|Endings:1
|Spacer|Width:600
|Text|Text:"C"|Font:StaffBold|Pos:8|Placement:AtNextNote
|Note|Dur:4th|Pos:-2
|Note|Dur:4th|Pos:-1
|Note|Dur:4th|Pos:0
|Note|Dur:4th|Pos:1
|AddStaff|Name:"Staff-1"|Group:"Standard"
|StaffProperties|EndingBar:Section Close|Visible:Y|BoundaryTop:10|BoundaryBottom:14|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
|Lyrics|Placement:Bottom|Align:Start of Accidental/Note|Offset:0
|Lyric1|Text:"These are lyr-ics\r\nand so are these.\r\n"
|Clef|Type:Treble
|TimeSig|Signature:4/4
|Note|Dur:4th|Pos:1
|Note|Dur:4th|Pos:0
|Note|Dur:4th|Pos:-1
|Note|Dur:4th|Pos:-2
|Bar
|Ending|Endings:1|Visibility:Always
|Spacer|Width:600
|Text|Text:"C"|Font:StaffBold|Pos:8|Placement:AtNextNote
|Note|Dur:4th|Pos:-2
|Note|Dur:4th|Pos:-1
|Note|Dur:4th|Pos:0
|Note|Dur:4th|Pos:1
!NoteWorthyComposer-End
Mike