Consider copying/pasting from the Resurgence Greek Project online: http://www.zhubert.com/ It's free, and everything is fully Unicode. If that gives you the same problem, then sounds like something's funky with the OS, but I'm not sure what. Otherwise it's Gnome Sword that's the problem.

I’m trying to get my Unicode fonts to work in Ubuntu, but I’m not having much luck. I’m not running GNOME – I’ve replaced it with LXDE, so it’s much smaller and faster.

The program I’m really noticing is Xiphos / Gnomesword. I’ve been trying to get the accented Greek and Hebrew fonts to display for about two years, and I’ve never been able to figure it out.

Have you? when you fire up gnomesword, and display a Greek text, do the accents show up? I have the Gentium font installed, but still no accents. Help!

Since Ubuntu 8.10, Greek Polytonic works out of the box when you simply select the Greek Polytonic layout. In previous versions of Ubuntu Linux, you had to make invasive changes with the Compose file, and GTK_IM_MODULE. Such changes are now unnecessary.

It is possible to get Greek Polytonic with SCIM, however this requires to install a large set of additional packages, including the manual installation of a ‘keyman’-style Greek Polytonic layout (not available in the Ubuntu packages). The default installation of SCIM does not provide even modern Greek writing support.