I added a match line to the gtkrc files for each of the respective Nodoka themes; however, I am not certain that this fixes the actual problem, as this doesn't seem to happen in other theme engines.

The problem is indeed in the gtkrc file. While panel bg is derived from fedora-default style, the fast-user-switch-applet uses bg set in fedora-menubar and panel menu uses bg set in fedora-panel-menubar. I've already managed to fix this locally for Nodoka-Looks and will upload the fix to git while all themes are fixed.

Fixed in git.

Now, the volume control, network monitor, Tomboy, and trash applets have a background of #ece9e9, and the rest of the panel/panel applets have a background of #f1eeee. As well, some other quirks have appeared, such as that the Show Desktop button and the Date/Time applet button are run up to the edge of the panel, which I am not certain if is desirable.

Hm... This shouldn't be happening and for me it is not happening. Wonder where the problem is... Just to be sure, I'll rebuild new rpm from latest git snapshot and add a srpm of it on my fedorapeople page.

OK, it does appear now. The fix to this would be to change the fedora-menubar style to not override bg[NORMAL] and getting rid of the patch, then all should be working fine... Or, we would need to make better matches so that we could effectively have whatever panel bg colour we'd like...

The srpm is here:
http://mso.fedorapeople.org/nodoka/gtk-nodoka-engine-0.6.99.1-0.7.git.bea309a.fc8.src.rpm

This time it should work. Check git 0995907

SRPM: http://mso.fedorapeople.org/nodoka/gtk-nodoka-engine-0.6.99.1-0.8.git.0995907.fc8.src.rpm