I have my logon script configured via Group Policy. I believe that it is only GPO configured scripts that are affected, if you're using the oldskool Active Directory user account configuration then it seems...
GPO Login Script. Table Of Contents. Presentation. Implementation of a logon script. Logon scripts are usually in batch or vbs format, it is also possible to run PowerShell scripts.While the Run logon scripts synchronously Group Policy is enabled (in the Computer Configuratio or User Configuration policy folders), the system ignores this entry. The Run logon scripts synchronously setting is stored in the values of RunLogonScriptSync (HKLM) and RunLogonScriptSync (HKCU).