As I mentioned earlier, I am using the Arduino IDE Serial Monitor to send strings over Serial.
Thank you for the array terminator reminder, and I apologize for the random Serial print outs, they just help me debug. This is just a stripped down version of my code to isolate the problem, I swear it all makes sense when I put it together. 
Your method seems to work PaulS, because I am now filtering for \n and \r characters, but that doesn't really explain why that \n character should be there in the first place if I never sent it...
The reason I had the Serial.flush function was to make sure that I cleared the buffer of any extra characters that may have come in with the Windows carriage return at the end of the string ie. \r\n. That however doesn't seem to work either,the only logical explanation I can come up with is that the \n character gets left behind in the Serial buffer so that the next time there is data to read it is the first character in line to pop out.