I have my panel vertikally aligned on my center screen. With 4.4 all icons got arranged vertically in th icon-box applett. Since I upgraded to 4.6, the icon are arranged horizontally, which makes all but the first invisible on my ~50 px wide vertical panel. No idea how to fix unfortunately, any patches welcome for testing.
You've probably noticed a bug that was caused by gtk 2.16. Please update the version 4.6.1.
I have the same problem on my Xubuntu 9.04. Did anybody tested 4.6.1 ? Does it fix the problem?
I installed XFCE 4.6.1.- Icon Box works fine. Thanks for fix.
Move bug to Window Buttons; the merge of tasklist and iconbox.