I found out what was causing several issues with my Space Age installation, including Steam API error

[Vesperon]

I am posting this to potentially help anyone who might have the same problem.

Since I installed Space Age, I was having these issues:
1. Factorio was no longer using %appdata%\Factorio for saves. I had to search my PC for a word from my save file name to find them in some weird folder (C:\VTRoot\HarddiskVolume3\).
2. Copying text from the game (even via the ingame Copy button) stopped working, so I could not copy my map seed or exchange string.
3. "Steam error: Couldn't initialize Steam API. Steam-related features are disabled.", so Steam achievements were not working.

Finally I found out that my security software (Comodo) was sneakily running the game in auto-containment, without me noticing it. It was playable, but it had these weird issues. So I turned off the auto-containment and that was the solution.