If you compare the notification area icon for Tomboy on a 32-bit 64-bit Ubuntu install you will notice that the icon is transparent on 32-bit but not on 64-bit. After further investigation, I believe this is a bug in the gtk.statusicon class of the mono gtk-sharp library. If you, for instance, compile and run the example found at http://www.mono-project.com/GtkSharpNotificationIcon, the same problem appears.
ProblemType: Bug
DistroRelease: Ubuntu 10.04
Package: tomboy 1.2.2-0ubuntu1
ProcVersionSignature: Ubuntu 2.6.32-30.59-generic 2.6.32.29+drm33.13
Uname: Linux 2.6.32-30-generic x86_64
Architecture: amd64
Date: Mon Oct 31 11:48:47 2011
InstallationMedia: Ubuntu 10.04 LTS "Lucid Lynx" - Release amd64 (20100429)
ProcEnviron:
SHELL=/bin/bash
LANG=en_US.UTF-8
SourcePackage: tomboy
I downloaded and used Shutter to take a picture of the tomboy icon that is not transparent. Interestingly enough, the shutter tray icon is also not transparent on my 64-bit machine, and it appears to be written in Perl.