Eclipse Preferences does not save classpath variables
<p>I am running Eclipse neon IDE for Java Developers, however, this problem has been occurring on mars as well. Every time I open eclipse I am faced with the following two errors: 
- The project cannot be built until build path errors are resolved
- Unbound classpath variable: <em>I don't believe the name really matters</em></p>

<p>The issue I am faced with is that every time I open eclipse I have to go to eclipse -> preferences -> java -> build path -> classpath variables
where I can then add the necessary variable and link the .jar I need. This fixes the problem. However, if I then close eclipse and re-open it, the variable is no longer there and the error reoccurs. I'm unsure of why my preferences aren't saved when I close eclipse. </p>

<p>Additionally, there is another class path variable that I no longer need, but if I remove it and reopen eclipse, it is there again. The location of that variable does even exist on my computer anymore. Any help or advice on this is appreciated. Thanks.</p>