Do you really need to use JDK9? As far as I know, JDK9 is still not released, and there might be some issues with JDK9 and the libraries used by Eclipse (e.g. SWT). I suggest that you switch to JDK8 to see if the problem persists.
As a side note, the latest release of Netbeans (8.1) runs fine on the Oracle JDK8 on Freya, but Netbeans uses the Swing UI framework instead of SWT so it's probably a little more portable than SWT. Could be worth trying, and Netbeans is actually a really nice IDE for Java development (among other things). The native Maven support is reason enough to use NB instead of Eclipse IMHO, but it also has many other nice features that has kept me from switching back ever since 2006/2007. I suggest you give it a try unless your Eclipse/SWT issue has already been solved.