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Hi,
For #1, If you were trying to check in CAD files from Vault Explorer, you will get this error. This is because, there is an additional option in Tools > Administration > "Disable Check In of Design Files" being enabled by default. So, it is recommended that Check In needs to be done via appropriate CAD application.
For #2 & #3, I suspect that it is due to "Filestore" permission issue. Could you please try granting "Full Control" to the user "AutodeskVault"? Please refer the attached image for reference.
Regards,
Madhan