You may get the 'root element is missing' error message if some of the XML files from %localappdata%\Red Gate\SQL Prompt 10 are corrupted.
To fix it, please try the following steps:
1. Uninstall SQL Prompt
2. Copy your style and snippets folder and save in another folder
3. Delete the files in %localappdata% > Red Gate > SQL Prompt 10
4. Reinstall SQL Prompt
5. If necessary, copy the custom style files and custom snippets over to the newly created SQL Prompt 10 folder respectively