Josh, does reply 2 to
http://my.noteworthysoftware.com/?topic=5391 help?
If not, ask again, but please describe the song structure, i.e.:
AABA or ABCAB etc. where each letter represents a theme.
If you can go one step further, say exactly where you've placed each flow direction command, such as
Bar 1, Master repeat open
Bar 7 1st ending
Bar 8 Master repeat close
Bar 9 2nd ending, Section Close bar line
and so on. The extra information may help us replicate your problem, and then resolve it for you.
Alternatively, use
http://yousendit.com to email the file to yourself, then copy the download link from that email into your forum message. Up to 25 people could then download the file and see what needs to be fixed.