Ok, I found out that there was an error in the build script - the signing
process was being executed twice. The insignia does not handle the
extraction of already signed engine well and the behavior is the result of
it.

After removing the certificate from the extracted engine.exe, the values in
the burn section of this engine.exe are left as they were. After signing the
engine and reattaching it back to the bundle everything seems fine. But when
installing, the bootstrapper expects that those values were zero before
signing, so it zeroes them out and breaks the signature of the engine.exe.

That's it.
PePri



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