A few questions:
1. What Mame version will you be using?
2. Are you planning to use console emulators (NES, PSX, Genesis, Atari, etc)
3. What frontend will you be using?
it said that it only detected 1 gamepad.... any reason why it was not detecting two gamepads when I fired it up the first time with both player 1 and player 2 controls grounded and hooked up to the Mini Pac?
As far as I know, the MiniPac is a keyboard encoder, not a 2-player gamepad encoder, and will basically work like a keyboard under Retropie. Retropie sees it as one gamepad when you push a button down, unlike a 2-player Xin-mo gamepad encoder in which console emulators will see player one and two controls automatically based on the player-1 configuration.
If you're not using console emulators, and only using Mame, configuration in Retropie is pretty unimportant (except for using the controls in the EmulationStation/Attractmode UI) as you can do all of the Mame configuration in the 'tab' menu. If you're going to use console emulators, then there's a bit more setup required.
I have the ground from the controls going into Pin 9, and the ground from the mini pac connection going into Pin 39.
If I'm reading this right, it sounds like you're wiring ground to the GPIO, and also wiring the Minipac to the GPIO? If so, don't do this.
http://www.ultimarc.com/mp_inst.html The wiring diagram for the Minipac shows ground on the board. You do not need to ground the Minipac to the Raspberry Pi, and you do not need to ground the controls to the Raspberry Pi. The grounds from the controls should only need to go back to the Minipac.
If you have an encoder (like you do) you do not need the Pi's GPIO pins for anything related to the controls. The encoder takes care of this.
Just so I'm clear: All grounds from all your controls should feed directly back into the MiniPac's ground pin. The mini pac should not be connected back to the PI, except through the USB cable.
Regarding why some buttons would work, and others would not... id say first remove the grounding stuff to the Pi (which may not matter). If there is still issues after that, then post back.
Welcome to the boards!