The code looks like it is supposed to mark it but there is a minor bug. I have a patch that takes care of the problem for me.
Created attachment 92247 [details, diff] Patch for kernel.eselect A fully qualified path is being compared to a relative path. This patch should fix it.
Fixed in SVN. Will be fixed by 1.0.5 release whenever that maybe :-)
1.0.5 is out.