How exactly are you testing it? Remember once you saved your configuration, the line that was in the input field is saved in your database, it no longer gets "auto-detected". Auto-detection only works the first time when you have never saved the configuration of a theme. If you had i.e. getTemplateFile('bla.jpg') in there, then save config, it saves "/bla.jpg" (or an empty string). When you change the getTemplatEFile call in config.inc.php, this will never affect the display, because /bla.jpg is always read...
It works in < 2.0, but does not work in s9y 2.0.
An easy test: create a new theme folder which will contain a copy of 2k11. Copy 2k11 to this new folder. Modify info.txt so you can distinguish it from 2k11. Add an image, named header.jpg and place it in this folder. Change themes to this copy of 2k11. In the config options, before saving, the image SHOULD show up as a default, but does not.