I was typing a similar response, assuming you're on a Linux server.
On a Windows server the FTP uploads use a local user account, not an IIS (IUSR*) user account. Namely, they use the same user account you use to connect to FTP with. By default, the uploaded files only get full access privileges for the owner and read privileges for the Users group. However, the IUSR* accounts do not belong to the Users group, therefore making the file unreadable and unwriteable to the web server (since PHP runs either as a SAPI module or through FastCGI under the same IUSR* account as your site).
My observations are on IIS 7 on Windows 10 but it shouldn't be that far removed from Windows Server 2012. IIRC this behavior exists since at least Windows Vista which predates Windows Server 2012.
Nicholas K. Dionysopoulos
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