It's also extremely odd behavior that LimeWire does what I found the fix for in the first place!

Launching the LimeWire app should just be a GUI front end that tells the system:

java -jar /Applications/LimeWire/LimeWire.jar

Which it musn't be, because then there shouldn't be any problems with using either method. The app itself is definitely not just an alias to the Java call. It's much too big a file for that.

If LimeWire has problems with this, then LimeWire is being programmed extremely poorly. There are a number of other reasons for this being true, besides this. Read around the forums and you'll see.

People shouldn't be writing Java apps if they don't understand the basic idea of what Java is for.