Thank you for your post.
First, Windows Server 2012 R2 is not supported for FileMaker Server 13. Please consider reinstalling Windows Server 2012 Standard.
With that said, the backup issues you are having are not related to Windows Server 2012 R2.
How often are you performing full backups?
When a backup begins, it temporarily pauses the database file so the file can be backed up properly. You should consider timing your full backups when there is less activity. Is there a reason why you don't perform progressive backups to save time and increase performance?
Please read Knowledge Base Article #9646 for more information on improving FileMaker Server performance: