I recently discovered the reason why the inputs I was recording from the IR-receiver using my Rabbitcore was all mixed up. It had no apparent pattern to it, and the signals it was picking up from my television remote (from pressing the same button) were inconsistent.
It turns out that the timing that the IR-receiver is sending the information is different from the timing that my Rabbitcore was programed to receive. This means that the Rabbitcore was picking up the same signal more than once, and was also picking up signals when the output of the IR-receiver was in the middle of switching from high to low or low to high. Fortunately, since the clock of the Rabbitcore is faster than the IR-receiver, this means that I can solve this problem through modifying the software.