This might be a matter of PHP attempting to log in to MySQL from a different IP than the user is configured for accessing from. I've run into it where I had 'root' enabled for login from 127.0.0.1, but some stuff was trying to log in from the 192.168.1.X IP address, so MySQL refused it.
I ended up adding a login entry for every permutation of local IP address as a valid location: 127.0.0.1, localhost, 192.168.1.X, ::1, everything.
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