The PackToSingleExecutable.exe tool also updates the executable icons and version information (doing the same job as WindowsIconUpdater.exe with other exports). It's possible it has a bug when trying to do that with certain unusual configurations - maybe check what kind of icons your project has or if there's anything unusual in the metadata (project name, author, description etc.)
If you can reproduce the issue with a new empty project, please file an issue and hopefully we can fix it quickly.
One more thing to check: perhaps try temporarily disabling any antivirus you have installed when running PackToSingleExecutable.exe - it's possible an antivirus tool thinks updating an executable is suspicious and so blocks it, causing the tool to fail to complete.