So although it is working correctly, I cannot get it to show output no matter whether I run it from command line or not. It's got all the correct lib directories etc too. Idfk, I guess if it ain't broke don't fix it, but it's really odd that this is even possible

yes you can see the output, try this way:
(suppose that mcproxy.jar and its lib subdirectory are located in c:\med\)
1 - open an msdos prompt
2 - type this commands:
c:
cd \med\
3 - try this command:
java -version
does it work or you get an error?
if you get an error (looking at your screenshot), type:
"c:\program files\java\jre7\bin\java" -jar mcproxy.jar
else, more simply:
java -jar mcproxy.jar
I've tried this. I've opened command prompt, and done the java -jar mcproxy.jar and it always gives me the errors above, or tells me the file can't be accessed. It doesn't make any sense...
java -version gets me this:
Microsoft Windows [Version 6.1.7601]
Copyright (c) 2009 Microsoft Corporation. All rights reserved.
C:\Users\win7>java -version
java version "1.7.0_45"
Java(TM) SE Runtime Environment (build 1.7.0_45-b18)
Java HotSpot(TM) 64-Bit Server VM (build 24.45-b08, mixed mode)
C:\Users\win7>