The old (2.16) GTK version used in the Windows release does have some GUI drawing issues (like invisible text on selected menu items in Vista/W7 for example) that were resolved in 2.24 as a sideefect of work on updating the Windows native theme for GTK 3, so it would be advisable to update the GTK libraries for newer releases.
For now I simply deleted all the included GTK related libraries in the install folder and am using the global libraries I have installed on my system (2.24.10). This fixed all the issues and I'm not noticing any new oddities that would be caused by this, so it should be a relatively safe change. This could possibly be combined with updates for all the other related things like pygtk and pygobject.
Thanks for looking into the Windows rendering problems. I'll give 2.24.10 a try.
This can be closed as fixed. The new GTK version in 0.4.8 fixed all the bugs I was having with previous versions.