So a piece of my code is:
SendKeys.SendWait("{PGDN}");
This code is sending the number 3 to the program I'm using. The Page Down button, above the arrows on my keyboard is necessary for a program and it has a function... This key has a different function than the Page Down button on the keypad.
Is anyone aware of a way around having SendKeys.SendWait(...) send the Page Down button on the keyboard, rather than the "3" on the numpad?
So my conclusion was quite simple. Using the InputSimulator as TyCobb recommended, I was able to properly simulate virtual key codes, and everything was smooth.