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Nothing weird, that's just how Windows works.

The cloudbase-init MSI uses a x86 python interpreter (until now we kept a single x86 one for both x86 and x64, but we're moving soon to a separate x64 interpreter for the corresponding MSI). This means that under Syswow64, the os's system32 directory is named "sysnative", eg c:\windows\sysnative. Similarly, an x64 executable can access the x86 system32 as c:\windows\syswow64.