Oh, I see. I misunderstood your situation. I had a similar issue with an application not being able to detect .NET Framework because it couldn't read a registry key that was supposed to be readable from the VOS (WriteCopy/Merged). I was able to resolve the issue by forcing the isolation mode for the needed registry keys in the ThinApp's registry files. If this is a project you can share, maybe I can have a look at it.
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