You may get the following message box when comparing two text files using SourceAnywhere for VSS:
The files that you are trying to compare are specified as binary in Visual SourceSafe (VSS). Visual SourceSafe doesn't always recognize Text file types properly. Even it is Unicode UTF-8.When Check-in files with 'auto' type, it would treats them as binary.
You can change the file type to Text by right-clicking the file -> Properties -> General tab in Visual SourceSafe (VSS).