When a fax is sent from a Windows 2012 R2 server, the output is shrunk to a quarter of the original size and centered at the top of the page. This can be seen in the transmission reports and also in the .tiff files found in C:\Program Files (x86)\GFI\FaxMaker\data\attachments location.
Windows 2012 R2 server
The 2012 R2 server needs the Microsoft KB2914011 update rollup which was launched to improve performance and reliability for Windows RT 8.1, Windows 8.1, and Windows Server 2012 R2.
Install the Microsoft January 2014 Rollup KB2911106 for Windows 2012 R2 and Windows 8.1. Once done and rebooted, the faxes should return to its standard size.