Alrighty, so I've done as you both have suggested. The serial monitor from the Arduino IDE appears solid. Really really wish they allowed copy and paste just so I could get a count of how much data was transmitted. In a bothersome but typical fashion the JAVA interface I've made for handling the Arduino serial commands is causing some issues.
The Arduino IDE's serial monitor appears to be working great. However, when I try and catch the data from my JAVA application it's almost like there's an endless loop going on or something is caught up. My pulse counts never reach the condition for ceasing the measuring operation, even though data is being transmitted? Bizarre. Maybe it's my fault? Shouldn't be RXTX, as I copy and pasted the one for my application directly from the arduino dependancies or lib folder if I recall correctly.