The is a bug cuasing caja to spawn lots of windows. Sabayon overlay have a fix at https://github.com/Sabayon/mate-overlay/tree/master/mate-base/mate-file-manager please add this patch to gentoo
Thank you for reporting. Backported 4f1e756e08e61840eb9a52de4debee30006ea31e. + 03 Apr 2014; Tom Wijsman <TomWij@gentoo.org> +files/mate-file-manager-1.6.3-r1 + -fix-x-caja-desktop-multiple-windows-issue.patch, + +mate-file-manager-1.6.3-r1.ebuild: + Revision bump. Backported x-caja-desktop issue solution to fix unnecessary + multiple windows popping up. Fixes bug #506660, reported by Joakim Tjernlund; + backport inspired by infirit.
Wow, that was fast! I wonder if mate-1.8 will added just as fast :)