Hey TheLuiz,
Short version is, it's a bug - someone else also pointed this out to me. If you right click - Run As, it launches the program from the root directory (C:\system32) instead of the project folder, which causes it to look for the folders in the wrong location. I will be fixing this in the next version, but for now you need to either:
A) Run the .jar program from the command line, navigating to the project folder first, or
B) Double click to run the .jar, assuming you have the file association set to run .jar files with Java(TM) Platform SE binary by default. You can change this in Control Panel - Programs - Default Programs - Chose Default Programs by File Type, then scroll down to .jar
Technically putting the PBS in the System32 will work but I don't really recommend that. Also, if the program doesn't seem to do anything when launched it's probably getting an error on something in your PBS (it's kind of not very good at handling non-vanilla Essentials stuff at the moment, which is another thing I'm working on improving). There are ways to work around it, but first you'll have to see what the error is by running via cmd (also going to be fixed to be less annoying). Sorry for the inconvenience, the current version definitely has some issues to iron out. I think I'll try to get a smaller update out to address some of these annoying problems more quickly.
Edit: The error where selecting right click - Run As causes it to search for files in System32 has been fixed in version 1.21 & onwards.