I'm using tint2 for my systray but when a file operation is done in thunar, there is a 'blank' let after the operation. After some searches and talks with the guys from tint2, it seems it's a bug in gtk+ and the status icon visibility has to be set to FALSE before unreferencing (see https://bugzilla.gnome.org/show_bug.cgi?id=589860).
In attachment, there is a patch that corrects the problem in setting the visibility of the icon to FALSE before destroying it.
Created attachment 3225 set the visibility of the status icon to false before destroying it
Fixed in master: commit 8a9a5174448ff5699f6935c04b3c86642634fb92 Author: Jannis Pohlmann <jannis@xfce.org> Date: Mon Dec 6 10:34:51 2010 +0100 Hide status icon prior to destroying it (bug #6891). Patch by Xavier D. This appears to be a bug in GTK+. If the status icon is not hidden before it is destroyed, it will sometimes not disappear (the notification area will never receive a "removed" signal). For more information please see http://bugzilla.gnome.org/show_bug.cgi?id=589860
*** Bug 6852 has been marked as a duplicate of this bug. ***