Usually when I create a Drupal site I set the admin theme to Garland: it saves time if I don't have to theme screens only a few people will use. But not all the admin pages will use Garland, so one time I started using Taxonomy Theme to encourage them to appear the way I wanted.
While developing one particular site I was trying to configure a block in Drupal. I just couldn't get it to appear anywhere: I tried all the regions, making sure that the block would appear on every page to every vistor. No joy.
However, the block would appear on the admin pages, even though the block was set to appear only in my custom theme, not in Garland.
The culprit? Taxonomy Theme. A wonderful module, I use it often and I'm grateful to Thilo Wawrzik for creating it... but because I had set it to display all the admin pages in Garland, the blocks page assumed I was arranging blocks for Garland, not my custom theme (on reflection, that's fair enough). Only when I switched the block admin screen to my theme did it work properly. Moral of the story? No idea, I leave that sort of thing to Aesop.