Java Certificate Issues
Literally right after typing this question up, my coworker found the solution.

Apparently, the "JAVA_HOME" variable changes based on the context of where you ran your jar. If you run the application directly, the variable leads to 

/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home


Whereas running it from bash/terminal/eclipse causes it to be located elsewhere

What this means in the context of this problem, is that we were not adding our certificates in all of the places necessary. Should you come across this, please verify that you are adding your certs in the correct locations.