Most of this is the fixes applied, yes. Don't know about these, but they appear harmless:
Added file: .\eb configuration.lnk
Added file: .\eb multi player.lnk
Added file: .\eb preferences.lnk
Added file: .\eb single player.lnk
Added file: .\persistent_logs\ai_subterfuge.txt
Added file: .\persistent_logs\issued_advice.txt
Added file: .\persistent_logs\issued_ancillaries.txt
Added file: .\persistent_logs\issued_traits.txt
I don't think this is the reason for your problems, sorry. The ones you play with need to have an identical validation result though, except for these lines above.