I am getting this warning when I shut down and then open my M1 Mac.
I use Bitwarden. It is not open when I received this warning.
It may not be open, but it is running, yes? That could be the problem. Some apps are poorly written and keep input locked even after they close the window. There's nothing KM can do in those cases. You have to close the app completely if that's the problem.
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This is a Mac OS feature that kicks in when the system thinks some app is automating the typing of passwords or other inputs like hot keys are being used. There is no way to permanently disable it for any app. But the fix is usually to put the Mac to sleep and then wake it again. If that doesn't work a restart should work.
This is not something that Keyboard Maestro or Bitwarden or 1Password or any other app has any control over - just something we have to live with as part of Mac OS. The important thing is that it is annoying but nothing serious is going on.
The Help (Secure Input Problem assistance) explains the issue.
In this case, the system is reporting that Bitwarden is the process that is holding the Secure Input Mode, so it is likely there is some background Bitwarden process involved.