I have a panel PC on which I'm running a custom build of Windows Embedded Standard. On maybe 1 out of 10 bootups, the system freezes shortly after the Windows blue background is displayed:

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Just blue and a mouse cursor, but it can't be moved and the keyboard is unresponsive to everything (no caps locks lights, etc)

What is the best way to go about debugging a freeze like this? Keep in mind that this build of Windows Embedded Standard is very bare-bones. I purposefully stripped out most of the typical Windows services since the purpose of this PC is simply to run a .NET app.

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Try my answer here to troubleshoot boot or logon freezes.

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