That about says it, doesn't it?

I was building a module for a site I'm working on, and I gave a module the same name as the current theme. One of the modules purposes was to make some blocks for the sidebar, so I included an implementation of hook_block() in the module. In Drupal development, this means you called the function modulename_block() -- if you already have a theme by this name, Drupal could also see this as themename_block(). Anyway, when I enabled the new module, all blocks on the page were gone. This is an issue other developers have seen, and the advice seems to be "don't do it".

So don't do it. I broke the block functions out into a separate module with a different name, and all was well.