To resolve this issue do the following steps:
1. Create a new folder named 'iPod Temp' (Folder > New).
2. Move all the notes in your current iPod folder(s) into the iPod Temp folder.
3. Select each iPod folder(s) and choose Folder > Delete.
4. Choose SOHO Notes > Empty Trash.
5. Click the action button at the bottom of the folder list and choose 'Recreate Default Folders'. A new iPod folder will be created.
6. Move all the notes from the iPod Temp folder into the new iPod folder.
7. Select the iPod Temp folder and choose Folder > Delete.
The iPod Sync command should now work correctly.