Final Pay check inquiry?

Hi I worked for this BDO co. for more than 6 years and I resigned first quarter of this year and tendered 2 weeks notice. My question is on my final pay check they said it will be released 60 days after I submitted all the necessary exit documents. I did but they are late in releasing my final pay check and it was indicated that my gross pay is more than 30k however I only received a final pay check for 12k an d they said that my SSS loan is not yet deducted to my final pay. Please enligtened me. I already wrote to them but they are saying that I should not look on my gross pay but just on the net pay.

if you believe you are entitled to more, the proper remedy is to file a money claim at nlrc