You are obviously looking at Eclipse's Project Explorer view. Look instead at the underlying directory structure using your OS' file manager. If I understand correctly, you have:
projectname/src/some.jpg
projectname/src/some.properties
Is this correct? (There is some confusion in my mind because your posts mentions a pictures folder)
While you are in the file manager, also look in the bin directory. That's where .class files go by default. Check to see if the properties and .jpg files got copied there. It's the bin directory that is used to build the final JAR.
Also, does the executable JAR contain additional JAR files? If so, are your pictures and properties in any of them? When Eclipse creates an executable JAR it places nested JAR file within it and adds a special classloader to load the nested JAR files. If one of the nested JARs contains the properties and pictures, then mist likely that classloader code is having problems. Of course, that could be related to how you access the properties and pictures (I do hope that you are using one of the load as resource methods.)
Personally, I would not do this. I always use
Maven (or at times Ant) to build my projects. I would either package all of the JARs I need in a lib directory and provide a script that sets the classpath accordingly. Or if I wanted an all-in-one JAR file, I would extract the contents of all required JARs and include their contents in my JAR (thus no nested JARs and no need to a special classloader). Both of these are easily accomplished with Maven and Ant.