it is common for scripts to work when you run them but not as a Startup script. When a Startup script runs there is no user. Startup scripts run with System privileges on the local computer, but with the permissions of the computer object elsewhere in the domain. The most likely cause is that the computer object (computer domain account) lacks permissions in the share. If all computers need permissions, you can grant the permissions to the domain group "Domain Computers".
Also it may be worth adding the actual filename to the end of the copy command as scripts like completeness.
One other thing is where are you deploying it in the gpo - user config or machine config and have you got the gpo running both types of script ( you can be selective so check whats selected ).
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