Recently, Eclipse started ignoring clicks on dialog buttons for me. This seems to be due to some changes in gtk 2.18. It does not use native windows for all widgets anymore, and SWT seems to rely on it.
Thanks to this blog post, I have this fix in my bashrc:
alias eclipse="GDK_NATIVE_WINDOWS=true eclipse"
The Debian bug tracker also knows about this problem, which is partly fixed for the eclipse packages. Bad luck that I am using a download from eclipse.org.