Our recommendation is contacting your local support in order to obtain further assistance on your inquiry. You might have received a refurbished working motherboard with cosmetic defects and that will not affect performance that is the reason why it shows like that. Regarding the beeping sound, test the system out of the chassis over a non static surface on a minimal configuration to narrow the issue.
Thank you very much for your reply. I will definitely do so and inform you if I encounter any problems regarding this in future.
Dr. Karun Kumar