Alarm code help!!!

AAARGHHH!!!!!!! I'm stuck and I have no idea why!!!!
Isn't that such a wonderful feeling?

So I've got this relatively complex burglar alarm system that I am in the process of making more permanent. I got it to work with all the bells and whistles and wall wiring on my Uno, but I bought a Pro board for keeping my Uno safe for other projects. This alarm system has got a button for arming, an "Armed" LED, a PIR sensor, keypad, buzzer, and LCD, so that each and every I/O pin is in use.

So I got the entire system working really well with my Uno and I haven't changed the sketch a bit since. Upon uploading to my Pro board, the keyboard will not register! I have NO idea why not! I know it's not a hardware issue, because without moving or barely even touching the system and an upload of a sketch that tests the keypad, I get positive results. So what's the issue?????

Here's the codes https://sites.google.com/site/midfreqaudio/home/arduino-forum-code (I didn't have enough character space, so that's a link to my website)

This worked great with my Uno (no changes since), but not with the pro.

So if you have any suggestions on what the heck is wrong, your help would be greatly appreciated!!!

There are a few differences.
I suppose you have a 5V 16MHz Pro board ?
The digital pin 0 and 1 and 13 are slighty different. What is connected to them ?

Yep 5V 16MHz pro.

dPin 0 is connected to the "armed" LED
dPin 1 is connected to the relay controlling the bright lights and loud bell.

They both work fine when I send those pins the blink sketch, so I assumed that they'd work in this situation as well.

The keypad (snippet from sketch)

const byte ROWS = 3; //Kind of wonky keypad, sorry!
const byte COLS = 4;
char keys[ROWS][COLS] = {
  {'9','8','7','#'},
  {'6','5','4'},
  {'3','2','1','*'},
};
byte rowPins[ROWS] = {5, 4, 3};
byte colPins[COLS] = {8, 7, 6, A2};

Thanks for your help already!

What about pin 13? If you use it as input, that might be a problem since the Pro board has a led on that pin.
Do you have a multimeter to check to 5V voltage of the Pro ?
I can not thing of anything else.