In TaskPaper versions up until 2.1 you didn't need to indent tasks and notes under projects for those tasks and notes to belong to the project. Tasks and notes would belong to a project even if they were at the same indentation level as the project. But in version 2.2 (still in development as of Jan 8, 2009) the file format is changing so that it's required that you indent those tasks under the project for them to be considered part of the project. This script will convert a document from the old style format to the new style format that requires indentation:

tell application "TaskPaper"
    tell front document
        repeat with each in entries
            if not (entry type of each = project type) then
                set text line of each to tab & text line of each
            end if
        end repeat
    end tell
end tell

See this forum topic for more discussion on the change.