[deleted comment]

$ yaourt -Qs python
extra/dbus-python 0.83.0-2 
     Python bindings for DBUS
extra/gnome-python 2.28.0-1 
     gnome-python is a set of interfaces to gnome-libs.
extra/gnome-python-extras 2.25.3-2 
     Gnome Python interfaces for libraries not part of the core platform
extra/pycairo 1.8.6-1 
     Python bindings for the cairo graphics library
extra/pygobject 2.20.0-1 
     Python bindings for GObject
extra/pygtk 2.16.0-1 
     Python bindings for the GTK widget set
extra/pygtksourceview2 2.8.0-1 
     Python bindings for gtksourceview2
community/pyopenssl 0.8-1 
     pyOpenSSL is a Python interface to the OpenSSL library
extra/pyorbit 2.24.0-2 
     Python bindings for ORBit2
extra/python 2.6.3-2 
     A high-level scripting language
extra/python-mpd 0.2.1-2 
     Python MPD client library
extra/python-notify 0.1.1-6 
     Python bindings for libnotify
extra/python-numpy 1.3.0-2 
     Scientific tools for Python
extra/python-urwid 0.9.8.4-1 
     Urwid is a curses-based user interface library.
extra/pyxml 0.8.4-6 
     Python XML parsing library.
community/tagpy 0.94.7-1 
     Python bindings for TagLib
community/zsi 2.0-3 
     a Python package that provides an implementation of SOAP messaging

I'll have to test it, more thoroughly but so far I have not encountered this 
issue.
Perhaps there's a new matching implemented in the latest release.

Can you try a similar theme (i.e. Dust) and confirm whether the same behavior
persists there?

@perfectska04:
I tried both shiki colors v4.5 and dust v0.4.1 with the same issue.
Some threads on Arch Linux forums for more details:
http://bbs.archlinux.org/viewtopic.php?id=82127
http://bbs.archlinux.org/viewtopic.php?id=82410

Updating to shiki colors 4.6 didn't solve the issue.

If the issue is also available in Dust, then it might be application related or 
due
to changes in gnome-panel.

To confirm this, can you try testing with the "New Wave" theme? It generally has
looser panel matching options, so if it also fails at drawing the correct 
background
- the issue might be elsewhere. If the background does appear with "New Wave", 
then
Shiki can be made to use looser matching types in order to fix the issue.

New Wave shows the same defect. Maybe GTK 2.18 are responsible of this.

If New Wave shows the same, then there are two possible reasons:

1. It's a gnome-panel/GTK 2.18 issue.

2. A new type of matching has been implemented, and those specific applications 
use
it. If this is the case, it can probably be fixed - but there's no way for me 
to know
which matching rule is being used.

Am I correct in guessing that the applications suffering from this the most are
sonata and gajim? If so, I'll install them and try various wildcard panel 
matchings
and see if one works.

Update:
I just installed both Sonata and Gajim, yet the tray icons seem to all work as 
intended.

This is on Ubuntu's GNOME 2.28. Perhaps there's an affected package in Arch 
that is
causing this issue?

Could be, I opened this bug: http://bugs.archlinux.org/task/16726
Thanks ;)

Thanks for filing the bug. I'll mark it as invalid, as it appears to be 
specific to
another Arch package and not the theme itself, as I've not been able to 
reproduce it
and it affects many other themes.

Feel free to comment further if the bug is resolved, or if anyone mentions a 
possible
workaround that can be applied from this end.