It looks like there is an issue with your form validation... you have:
$WAFV_Errors .= WAValidateNM(((isset($_FILES["V1Pru"]))?$_FILES["V1Pru"]["size"]:"") . "",0,52428800,0," ,",true,5);
$WAFV_Errors .= WAValidateNM(((isset($_FILES["V1Cert"]))?$_FILES["V1Cert"]["size"]:"") . "",0,12582912,0," ,",true,5);
The last argument is the identifier... so you have them both set to: 5
They need to be unique and match the show IF code.... your show if code looks like it uses identifiers "1" and "2", so the code should be:
$WAFV_Errors .= WAValidateNM(((isset($_FILES["V1Pru"]))?$_FILES["V1Pru"]["size"]:"") . "",0,52428800,0," ,",true,1);
$WAFV_Errors .= WAValidateNM(((isset($_FILES["V1Cert"]))?$_FILES["V1Cert"]["size"]:"") . "",0,12582912,0," ,",true,2);