I had been using Xfce 4.4 on Xubuntu 8.10, when I upgraded to the 4.6 beta through the developer's ppa on launchpad. If xfconf is not installed, the panel looks normal (other than a lack of theming). I noticed that MCS had been replaced by xfconf, so I installed that, which brought my old GTK theme back. However, the "Applications" and "Places" buttons were stretched to fill almost the entire top panel, pressing my quicklaunch buttons up against the statusbar. A simple workaround is to just enter the panel editor, change the panels size to one pixel larger, then back. Put this under Xfconf, as it seems to be a problem with settings migration rather than with xfce-panel itself.
Created attachment 1921 Panel buttons stretched after upgrading to 4.6 beta
This has nothing to do with xfconf, as the panel doesn't even use it. Please just report bugs where you see them, not where you assume them to be.
No idea what is causing this, but going to mark this as fixed once the devel panel enters master because it has a completely overhauled and improved plugin allocation code.
Devel branch has been merged in master. A 4.7.0 release will follow soon. If you think this bug is not fixed? Feel free to reopen the bug.