If you would like to tweak the jfacefonts.properties file to settings that are appropriate for FreeBSD and contribute the changes back to us, I will post the file on the Eclipse UI team web page.
The initial font settings are found in the jfacefonts.properties file (and platform-specific variants) in plugins/org.eclipse.jface/jface.jar.
Eclipse Platform UI Team Lead
Just to let you guys know. I 'deinstalled' the M4 version of eclipse.
Installed the M5 version and no problems. Everything works fine, it does
complain about missing fonts, but that is it. So it could have been in the
M4 version in combination with FreeBSD.