After posting a bug report to Eclipse bugzilla I got some replies to it. It turned out that something got corrupted during my installation and I suspect it was due overheating hard drive. The machine I have been working on is a compact Dell XPS 210 desktop and I was shocked when I saw its hard drive temperature. It was 82 C degrees which is quite a lot for a desktop drive. Well, if you take a look at its internals you will see that it is not really a layout for a proper work station.

With some searching I found i8kutils which is meant for Dell laptop but I managed to force the case fan to run with full blast with it. This dropped temperature somewhere around 60. I have no clue how long that has been going on as the machine was used by other developers before me. SMART status was not showing any error so I hope the drive is still usable.

To solve the problem with crashing Eclipse I decided to try out reinstalling gnome packages. I basically did that to all installed gnome packages and surprisingly Eclipse was stable after that. And that took me only couple working days... apparently I have become system administrator in addition to my existing Java developer title.