A common error message that users experience points to a "versioning problem" as shown below:
This error can appear for a few different reasons including file saving problems or other instances of file corruption, as well as version problems. Updating Scaffold to the newest version may not fix it. Additionally "version" can be related to both the version of the program and the version of the file itself (program internals). If updating the program does not get rid of the error message, please contact support via email at support@proteomesoftware.com as additional investigation is needed. We will work to diagnose the problem as quickly as possible.