Uploading Sketches from Windows Command Line
Turns out that the Ignoring Bad Library Name error that I had been receiving regardless of if I ran Arduino IDE through command line or standalone was the issue. For whatever reason it was blocking the script with a dialog that then failed the upload regardless of if I manually moved through the popup. 

Final setup for those looking for this in the future:

Windows 8.1 x64 with Arduino IDE version 1.5.6-r2(I will revert to 1.0.5 and test with that, and report results) using a Leonardo board. Command is as follows:

Working Directory: C:\Program Files (x86)\Arduino

arduino --board arduino:avr:leonardo --port COM14 --upload C:\Users\Dev\Documents\Arduino\sketch_jun06a\sketch_jun06a.ino


EDIT: As promised, I attempted this with version 1.0.5-r2 and was unsuccessful. Potentially a 1.5.+ feature.