For others still having this issue - I fixed it by deleting BuildConfiguration.xml within %AppData%/Roaming/Unreal Engine/UnrealBuildTool/BuildConfiguration.xml.
For some reason the build config was specifying 14.29.3016. This must have been auto-generated at some point and was the cause of the issue. Maybe the GenerateProjectFile.bat should output that it is using a version taken from an xml file.