Glipper causes the faulty behaviour reported in this bug for Eclipse (the bug was marked WONTFIX there): https://bugs.eclipse.org/bugs/show_bug.cgi?id=153809
I use Gentoo, gnome and glipper-1.0-r2.
I also think Glipper may be the culprit for similar flakey behaviour in Nautilus where sometimes files aren't copied over (but nothing happens) on ctrl+v.