Do you know if that connector has the soldermask pads defined in the padstack?
How were the gerbers generated? If the SM pads are not in the padstack you would need to call out the bottom pads in the soldermask document.
Are the missing inner pads actually used? They may be getting removed if your setting say to remove unused pads.
Yes, solder mask pads for both top and bottom are defined in the pad stack.
Missing inner layer pads are connected to ground plane, The thermal spokes show up but pads do not.
I found that by adding the bottom layer pads to the bottom soldermask CAM setup I was able to get them to show up on the ODB++
But still no solution for the missing pads on inner plane layers.
So I sent the files to one of our contract layout designers and using the latest version of PADs and he was able to generate ODB++ files without any missing PADs. So I think the problem must be related to using the older 9.5 version.